There is a useful rule of thumb, when you have a proof by contradiction, to see whether it is "really" a proof by contrapositive.
In a proof of by contrapositive, you prove $P \to Q$ by assuming $\lnot Q$ and reasoning until you obtain $\lnot P$.
In a "genuine" proof by contradiction, you assume both $P$ and $\lnot Q$, and deduce some other contradiction $R \land \lnot R$.
So, at then end of your proof, ask yourself: Is the "contradiction" just that I have deduced $\lnot P$, when the implication was $P \to Q$? Did I never use $P$ as an assumption? If both answers are "yes" then your proof is a proof by contraposition, and you can rephrase it in that way.
For example, here is a proof by "contradiction":
Proposition: Assume $A \subseteq B$. If $x \not \in B$ then $x \not \in A$.
Proof. We proceed by contradiction. Assume $x \not \in B$ and $x \in A$. Then, since $A \subseteq B$, we have $x \in B$. This is a contradiction, so the proof is complete.
That proof can be directly rephrased into a proof by contrapositive:
Proposition: Assume $A \subseteq B$. If $x \not \in B$ then $x \not \in A$.
Proof. We proceed by contraposition. Assume $x \in A$. Then, since $A \subseteq B$, we have $x \in B$. This is what we wanted to prove, so the proof is complete.
Proof by contradiction can be applied to a much broader class of statements than proof by contraposition, which only works for implications. But there are proofs of implications by contradiction that cannot be directly rephrased into proofs by contraposition.
Proposition: If $x$ is a multiple of $6$ then $x$ is a multiple of $2$.
Proof. We proceed by contradiction. Let $x$ be a number that is a multiple of $6$ but not a multiple of $2$. Then $x = 6y$ for some $y$. We can rewrite this equation as $1\cdot x = 2\cdot (3y)$. Because the right hand side is a multiple of $2$, so is the left hand side. Then, because $2$ is prime, and $1\cdot x $ is a multiple of $2$, either $x$ is a multiple of $2$ or $1$ is a multiple of $2$. Since we have assumed that $x$ is not a multiple of $2$, we see that $1$ must be a multiple of $2$. But that is impossible: we know $1$ is not a multiple of $2$. So we have a contradiction: $1$ is a multiple of $2$ and $1$ is not a multiple of $2$. The proof is complete.
Of course that proposition can be proved directly as well: the point is just that the proof given is genuinely a proof by contradiction, rather than a proof by contraposition. The key benefit of proof by contradiction is that you can stop when you find any contradiction, not only a contradiction directly involving the hypotheses.