Dividing 100% by 3 without any left In mathematics, as far as I know, you can't divide 100% by 3 without having 0,1...% left.
Imagine an apple which was cloned two times, so the other 2 are completely equal in 'quality'. The totality of the 3 apples is 100%. Now, you can divide those 3 apples for 3 persons and you will get 100% divided by 3 and none left.
Is this because                                    1: mathematics is not real                   2: there is no 1 or 2, and it's in fact just an invention for measurements? So,  in the division of 100% by 3 WITHOUT any left, is NOT  accurate?
 A: Meanwhile in ancient Greece...
For quite a long time, greek (and not only) mathematicians described numbers as lengths of certain line segments. So, when asked "What is $\sqrt{2}$ equal to?" they'd draw a $1\times1$ square (nevermind the unit), draw it's diagonal and say "There it is! This diagonal's length equals exactly $\sqrt{2}$!". So to answer your question: draw yourself a line, pick up a calliper, and divide this line 3 times. Like so:

And there you have it: 100% of a line segment divided into 3 equal parts. And if you ask "Yes, but what is this $\frac{1}{3}$ really equal to?" ancient philosopher would show you one of the parts and say "There it is! This segment's length equals exactly $\frac{1}{3}$!"
A: There are a number of conceptual errors in your question.

In mathematics, as far as I know, you can't divide 100% by 3 without having 0,1...% left.

In mathematics, "100%" means nothing more or less than "100 per 100", namely "$100 / 100 = 1$. So in mathematics you can divide $100\%$ by $3$ without having $0.1\%$ left. $100\% / 3 = 1 / 3 = \frac13$.

Imagine an apple which was cloned two times, so the other 2 are completely equal in 'quality'. The totality of the 3 apples is 100%. Now, you can divide those 3 apples for 3 persons and you will get 100% divided by 3 and none left.

Here you correctly observe that if you consider a group of 3 identical apples, and count those apples as 100%, then you can divide that group up into 3 (equal) parts and get none left. As explained above, this is not contradictory to "dividing 100% by 3".

Is this because 1: mathematics is not real 2: there is no 1 or 2, and it's in fact just an invention for measurements? So, in the division of 100% by 3 WITHOUT any left, is NOT accurate?

No.
The mathematics concerning integers and rationals and real numbers is very real, in the sense that using purely logical reasoning we can from mathematical axioms prove rigorously and unambiguously many statements about integers and rationals and reals that can be interpreted as statements about real-world phenomena, and in such a way that these statements can be empirically verified. More specifically, this part of mathematics has both explanatory power and predictive power about the real world, meaning that it provides succinct explanation for phenomena that we have observed and that it allows us to predict future phenomena that we have not yet observed.
For instance, right now the webpages you are reading from https://math.stackexchange.com have been encrypted using RSA encryption, and the decryption process relies on Fermat's little theorem to be true when interpreted as a statement about large positive integers encoded in your computer in binary format (with the addition and multiplication operations defined according to how your computer does them)!
In other words: If Fermat's little theorem (interpreted as a predictive statement about your computer) fails to be true, then you simply would be unable to read these webpages!
It turns out that Fermat's little theorem can be proven in a suitable form in a mathematical theory called PA (First-Order Peano Arithmetic). And so far, every single known theorem of PA has not been found false under the standard interpretation as a real-world statement. So we definitely have good reason to believe that "mathematics generated by PA is real".
As for $1$ and $2$ being inventions, the abstract concept of the natural numbers as a model of PA (i.e. they satisfy all the axioms of PA) is indeed a human invention, but that does not necessarily imply that this abstract concept has no real-world meaning, as explained above.
To make it clear, 100% can be divided exactly by 3, both in mathematics and in a suitable interpretation of the concepts "100%" and "3" in the real-world.
~ ~ ~
Coming back to your mention of "$0.1\%$", it is actually due to a conceptual mistake. It is a (mathematical) fact that $100$ is not an integer multiple of $3$. That is, there is no integer $k$ such that $100 = 3 × k$. However, there is a rational $r$ such that $100 = 3 × r$. When we write "$100\% / 3$" in mathematics, we mean exact division, which in this case yields the rational number $\frac13$ as the answer.
If you punch a basic calculator (which is designed to show you only some numbers in base ten) and ask for 100% / 3, then you may get something like 0.333333333. Why? It is not because the answer is $0.333333333$. Rather, the calculator is unable to show the answer in base ten. Furthermore, if you set your calculator to round the answer to 3 decimal places, then you would instead get 0.333, only because you asked for the answer rounded to 3 decimal places! So the (mathematical) fact that $100\% = 0.333 × 3 + 0.1\%$ does not actually have anything to do with the division of $1$ by $3$.
By the way, this phenomenon involving calculators is an artifact of our choice of base system for general daily life, which influences the design of such calculators. This has nothing to do with the mathematical concept of division. If humans had only 3 fingers on each hand, we might have ended up using base six for daily life.
We can in fact show precisely what would have happened if we used base $6$. We (using base ten) write $21_6$ to mean the number represented by the string of symbols "21" in base $6$, which means $2 × 6 + 1 = 13$. Likewise, in base $6$ we would have $1 / 3 = 0.2_6$ because $\frac13 = \frac26$. Note that we also have $\frac13 = 0.333\overline{3}$, where the overlined "$3$" means that "$3$" is repeated forever. There is no contradiction here. Whenever we do not write the subscript on a number, it is by convention understood as a base ten number. To make clear, $\frac13 = 0.333\overline{3}_{10} = 0.2_6$.
A: One way to see this is to distinguish between definition and representation. I think you have began that.


*

*Definition: 1/3 is by definition exactly one third of 1.

*Representaion: "1/3" is a representation that is useful here. However there is no representaion of 1/3 using something like "0.3333333...". Unless you have an infinite paper or screen, of course. ;-)

*Another question, which you also asked, is mapping of the definitions to the real world. A very difficult question. However you could look at this from the aspect of usefulness. We measure something. That gives us a number. What can it be used for? How accurate is it? Will we get the same number the next time? Again a very difficult question - at least if we are outside the more obvious cases. This is today a big obstacle in science. (Read John P Ioannidis research to get touch of this.)


Good luck with your thoughts and investigations! :-)
A: The fundamental fallacy in your reasoning is that "natural == real". Just because a number never ends doesn't mean it isn't a "real" number with real application.
You have three apples. Three is a "natural number"; it is positive and whole, used in counting and other "everyday math".
Now, you are converting these three apples to "100%". "Percent" is from Latin per centum, literally meaning "per hundred", and so it defines a ratio with a common base; one hundred "per hundred" is everything; the whole. That's why the percent sign % looks the way it does; it's a symbol representing a fraction, that fraction here being the percentage quantity divided by 100.
Now, you have to ask (and the question doesn't), what is "the whole"? In this case, it's the three apples. You can't speak in percentages without speaking in percentage of the whole, requiring you to define the whole. 100% of three apples is three apples, and that's all there is to it.
Now, one-third of 100 is 33.3333... It is not a "whole", "natural" number, because 100 cannot be divided "evenly" by 3. This is utilized in the problem to offend our sensibilities, because one apple is a whole thing, and that's one-third of 100% of the apples. However, 100(%) means three apples; it's one hundred out of (divided by) one hundred of (times) three apples, divided by 3. The math, therefore, holds:
$$\dfrac{(\dfrac{100}{100} * 3)}{3} = 1$$
The question essentially intends to trick us by basically stating 100=3 and hoping we won't notice the switcheroo.
A: In the real numbers, you can divide any quantity by 3 and get 3 equal parts.  This is because of how we've defined the real numbers.
You pose a very valid question, though, as real numbers aren't the only way to model quantities.  For instance, we could also use the natural numbers (the ones we use for counting things discretely.)  For instance, if you were to consider all of the atoms present in an apple, the apple would only be divisible into 3 parts with the same number of atoms if the total count were a multiple of 3.  With that choice of representation, it's true that it may not be possible to divide an apple into three equal parts.

At the risk of creating confusion (spurring curiosity?), here is another interesting conundrum.  If you're sufficiently creative in how you cut up the apple, you can actually create two apples of identical volume from the single apple.  This follows from certain assumptions we'd really like to be true, but it's certainly a counter-intuitive result.  This begs us to question what we're taking for granted in our intuitive understanding and, indeed, whether our intuition is actually self-consistent.
A: 
So in mathematics, as far as I know, you can't divide 100% by 3, without having that 0,1..% left....  

No! we can in Math and also in real life. This is similar to ask can we divide $1$ into 3 parts? And the answer is again yes. $$1÷3=\frac{1}{3}$$ because adding $\frac{1}{3}$ three times give $1$.
Consider 3 sticks of same length. Align these three sticks and call the total length as 1 unit. Now the length of any of the individual stick is exactly $\frac{1}{3}$ unit.   
Moreover you can use the number system having base 3 to remove the (apparent) incompleteness of the base-ten expression $1÷3=0.333333333...$ In the number system having base 3, the number '3' itself will be written as $10$ and the number $1$ as it is.
The division $1÷3$ is now $1÷10$ which is equal to $0.1$. so you see writing (in base ten) $100÷3=33.333333$ does not mean that we cannot divide $100$ into three equal parts. What it means is that we are using a number system having $10$ base so we cannot write $\frac{100}{3}$ in decimals.
A: It's been answered above, but I thought I should try for a consise answer.
The fact that 100, in base 10, divided by 3 lacks a finite representation does not mean that it's impossible to divide 100 by 3.  
In fact most real numbers can not be represented by a finite decimal number.
A: The Apple LOOKS like it has been divided exactly into 3 pieces. It is impossible to divide a physical object using mathematical precision.
A: I guess it came out of confusion; Confusing the number 100 with the totality of something (100%, 1 unit) - However, the value 4 can be put into a unit and start being 100% of itself, you can divide 100% by 3 and get 1/3 and 0(»zero) left but you can't do it with the 4. -- I think, as @KeithS wrote I am making a switcheroo, although not intentional. 
As writting this I thought that maybe you can't divide always 100% of something into 3 equal parts without any leftovers. What if given object has 4 atoms, how do you do it?
As of writting the above I thought, one object (apple with 4 atoms for an example) / 3 is different from saying 3 (4 atomed apple)equal objects / 3.
And so, 100% can't always be divided by 3 without any left.
Also, the edit that was made to my initial post was important to the extent that explained it may be a dumb question (as I'm not a mathematician nor am I in the field) it was a problem that I thought of and as it seems to be now just confusion.
A: In reality you are approximating, but mathematics is more than reality so it prefer preciseness whenever possible.
Here $\frac{1}{3}\times100=33.333\cdots$ and $3\times 33.333\cdots=99.999\cdots$. I think this is what confused you. 

But $100=99.999\cdots$
Let $$x={\Large99.999\cdots}\\\implies 10x=999.999\cdots=900+99.999\cdots=900+x\\\implies10x-x=900\\\implies9x=900\\\implies x=\frac{900}{9}={\Large100}.$$
A: Here, in a practical way – I understand all your concepts, sirs – I was using a simple calculator on my computer, and looks like mine's got a 10 decimal digit precision. Which make this possible:
9 decimal "3s"
33.333333333 * 3
= 99.999999999
10 decimal "3s"
33.3333333333 * 3
= 100
If I divide 100 by 3, it'll give me 10 decimal "3s". And this expression was valid:
100/3 * 3 = 100
A: In base 10, no, not as long as you only allow finite digits. In base 3, we certainly can (or any other base divisible by three). 
A: The number 100 as the maximum percentage (unity) is nominal, just for people's convenience. We could have as well used 300% as one totality for three apples. So, we could divide it by 3 in base 10 and have 100% per apple.
