Maybe at some elite schools they may search out your application for this information, but the majority of schools wont care. Admissions committees are realistic and understand that scheduling conflicts occur.
- senior medical student / admissions committee interviewer
If you do one part of your science pre-reqs in the summer and everything else is good, you should have no problems. You mentioned you will be taking the course at your current undergrad institution, which is great. I took a whole year of physics over the summer and it definitely didn't affect me negatively in admissions. Best of luck to you