Many statements of mathematics are phrased most naturally in terms of multisets. For example:
Every positive integer can be uniquely expressed as the product of a multiset of primes.
But this theorem is usually phrased more clumsily, without multisets:
Any integer greater than 1 can be written as a unique product (up to ordering of the factors) of prime numbers.¹
Apart from rearrangement of factors, $n$ can be expressed as a product of primes in one way only.²
Every integer greater than 1 can be expressed as a product of prime numbers in a way that is unique up to order.³
Many similar factorization theorems are most naturally stated in terms of multisets; try a search for the phrase "up to rearrangement" or "disregarding order". Other examples: a monic polynomial is uniquely determined by its multiset of roots, not by its set of roots. The eigenvalues of a matrix are a multiset, not a set.
Two types that are ubiquitous in mathematics are the set and the sequence. The sequence has both order and multiplicity. The set disregards both. The multiset has multiplicity without order, but is rare in mathematical literature.
When we do handle a multiset, it's usually by interpreting it as a function into $\Bbb N$. This leads to somewhat strange results. For example, suppose $M$ is the multiset of the prime factors of some integer $n$. We would like to write:
$$n = \prod_{p\in M} p$$
or perhaps even just:
$$n = \prod M$$
But if we take the usual path and embed multisets in the conventional types as a function $M:\mathrm{Primes}\to\Bbb N$, then we have to write the statement with an infinite product and significantly more notation:
$$n = \prod_{p\in\mathrm{ Primes}}p^{M(p)} $$
(For comparison, imagine how annoying it would be if sets were always understood as characteristic functions with codomain $\{0, 1\}$, and if we had to write $\sum_{x\in S}{F(x)}$ all the time instead of just $|F|$.)
Interpreting multisets as functions is infelicitous in other ways too. Except in basic set theory, we usually take for granted that the difference between a finite and an infinite set is obvious. But for multisets-as-functions, we have to say something like:
A multiset $M$ is finite if $M(x)=0$ for all but finitely many values of $x$.
The other way that multisets are sometimes handled in mathematical proofs is as (nonstrict) monotonic sequences. One often sees proofs that begin "Let $a_1\le a_2\le\ldots\le a_n$; then…". The intent here is that the $a_i$ are a multiset, and if $b_i$ are a similar sequence of the same length, then the multisets are equal if and only if $a_i = b_i$ for each $i$. Without the monotonicity, we don't get this equality property. With first-class multisets, we would just say $A=B$ and avoid a lot of verbiage.
Sets and sequences both have a full complement of standard notation and jargon. Multisets don't. There is no standard notation for the union or intersection of multisets. Part of the problem here is that there are two reasonable definitions of multiset union:
$$(M\uplus N)(x) = M(x) + N(x)$$ or $$(M\Cup N)(x) = \max(M(x), N(x))$$
For example, if $M$ and $N$ are the prime factorizations of $m$ and $n$, then $M\uplus N$ is the prime factorization of $mn$, and $M\Cup N$ is the prime factorization of $\mathrm{lcm}(m,n)$.
Similarly there is no standard notation for multiset containment, for the empty multiset, for the natural injection from sets to multisets, or for the forgetful mapping from multisets to sets. If there was standard notation for multisets, we could state potentially useful theorems like this one:
$$ m|n \quad\mbox{if and only if}\quad \mathrm{factors}(m) \prec \mathrm{factors}(n)$$
Here $\mathrm{factors}(m)$ means the multiset of prime factors of $m$, and $\prec$ means multiset containment. The analogous statement with sets, that $m|n$ if and only if factors$(m)\subset$ factors$(n)$, is completely false.
It seems to me that multisets are a strangely missing piece of math jargon. Clearly, we get along all right without them, but it seems that a lot of circumlocution would be avoided if we used multisets more freely when appropriate. Is it just a historical accident that multisets are second-class citizens of the mathematical universe?