Question: Is it ok to use an "in" before "*in vitro*", or other Latin-derived phrases that start with "in"?

For example, could you say "there's been a lot of advances in *in vitro* fertilization lately"?

Answer: 
English has compound words that have an space where one might otherwise see a hyphen. Since *in vitro* is a loanword which behaves as a single lexeme, use it as such.

For purposes of euphony and clarity, I'd probably word it "advances within [the field of] *in vitro* fertilization".
It offends no principles of grammar or good usage that I am aware of, but if it discomfits you, try saying instead "in fertilization *in vitro*".