Is it appropriate to express concerns to a professor about a new exam format?
It’s totally appropriate to point out to your professor that your grade is suffering for technical reasons having to do with the online format of the exam. If your professor is reasonable she will not be in the least bit offended by this.

By the way, we are pretty much all dealing with issues of this sort nowadays. I experienced something similar just a few days ago when I gave an online quiz. One of the problems required entering the answer to a question in decimal notation, and this was automatically graded by the testing platform. The correct answer was 15/64=0.234375, but some students assumed it was okay to round off the answer and entered 0.234 or 0.23, only to have that marked off as incorrect. When they emailed me to point out the issue, I gave them the points for the question.

To summarize, let your professor know. Be polite and explain the technical issues in entering the answers that caused your answers to be marked as incorrect. If you explain it clearly and convincingly enough, not only will the professor be in a better position to design a fairer format for the final exam, she may actually give you back some of the points that were marked off in the current exam.