PTCAS does not verify that you have matched your core pre reqs, BUT does PTCAS make sure you have matched/labeled your other courses like math and English?
I'm not 100% sure, but I think they do. I remember reading in the instructions about how you have to input every since class correctly. Since they have to verify your GPA, they have to look at all your classes. I think that if you omit/mess up the input of your classes, it'd just delay you application. It takes like an hour. I went to 3 schools and though tedious, wasn't that hard.
I remember last cycle after I had entered all my classes, PTCAS changed some of the labels that I had placed on some classes. I suggest to enter the classes as you see them and as the verification process takes place they will adjust as needed.