For Biology 1M03 1D, I have selected C01 but for this core there are two available times. I preferred the later time but on my schedule, I was given a mix of both two from the earlier time and one was from the later time, but they are still both C01. How do you fix this?

I think they are all your core 1 calsses (i'm not sure what you mean buy you're given mix of both classes)

Some classes have 3 classes at same time (just different day), and some have 3 classes (different time)

If this is the case, you will have to have all those classes in your timetable. Hope this helps =S

You register by core number not times. C01 has more than one time because each class has 3 hours of class a week, you have to attend all of them, you can't pick and choose between them. You have to pick based on which C0# is better for you, not which time within that core number.