Would medical schools have problems reading multiple transcripts?

I'm considering taking one class during the summer and another during the fall at different institutions because of price differences. Would this be problematic?

Not at all! I did the Harvard post-bac two years part time while working. During the summer I took inorganic at U Mass because it was MUCH cheaper, and I took an EMT course at Northeastern. With undergrad plus the fact that I had taken calc during the summer at another institution (money reasons again) I had 5 transcripts total. Not one interviewer questioned me about it. You'll be fine. Good luck!