Contractions ("can't", "don't") in a mathematical paper

My experience has typically been that the more formal mode, with no contractions, is preferred for most scientific publications. It is not a terribly strong or important custom, however, and in one of my more high-profile multi-disciplinary publications, I actually found the copyeditor introducing contractions into my writing!

In short: worth mentioning, but not a big deal. As a reviewer, you might say something like: "I found the contractions distracting, and would advise removing them" but I wouldn't recommend being much stronger than that in your statements.

Leave copy-editing to the copy-editors, unless the issues with the writing affect understandability. If the journal has an opinion on whether contractions are acceptable, the copy-editors will deal with it.

Honestly, I don't (sorry, do not) see why the contractions could be a problem. They're (sorry, they are) completely comprehensible and it seems that your only objection is that you think there's (sorry, there is) a rule that says you can't (sorry, cannot) use them in formal writing. There is no such rule.

These matters will usually be regulated at the level of the journal's style sheet, which oftentimes will respect conventions of the journal's publisher. There are many other related issues apart from the use of contractions: single versus double quotes, British versus US spelling, etc. All of these technicalities are best left to the editors, while the referee should focus on the merit. Unless of course the journal's referee report form (if there is one) explicitly asks for comments in this area.