I was in a very similar situation as you were. I had Organic I, lab, Genetics, Mammology, Mam Lab, Parasitology, Parasit Lab, a gym class, and a scientific thesis class every science kid has to take. I was also an RA for the first time ever and worked in our C-store12 hours a week and had Pre-vet club. I straight up failed Organic lecture with a 55% and got a C in genetics. However, A's in everything else.
However, I did what everyone here is suggesting: I evaluated what I did and specific classes. I later found out that only 1 kid got an A in organic lecture, 5 kids got B's, 10 kids got C's and everyone else of a 40 person class got D's and F's. That's a pretty high fail rate. I knew I did not devote enough time to genetics because of organic. I debated on whether or not to be an RA (and senior RA this year) because of this. I decided to stay an RA because I knew that organic here is ridiculous because the professor is terrible. I wasn't about to give up free room and board because of one class.
At this point, I was eliminated right out the gate at 2 schools. However, 2 schools told me that I was qualified to be in the program, but others were better. I got an interview at my fifth school and am waiting for a letter of acceptance or rejection. A lot of other factors influence your chances of getting in. My RA position junior year and Senior RA position my senior year actually helped me, even though I failed Organic. I have retaken it (got an 85% the second time around), retook Genetics and got a B and I am retaking Dev Bio. I had pretty good GREs and thousands of animal experience hours, but just over 100 vet shadowing hours. There's some obvious points that hurt me, but others that help a lot. Grades are only one factor and I can't stress that enough from my personal experience.
I would say that you evaluate not just how much time you spent on classwork, but how you spent that time. Study smart, not study hard sort of thing.