Am I wrong or does the storyline with Zack have a major hole? (spoilers)

well, at 15 they would be freshmen, or sophomores... depends on the month of their birth and which semester... that lines up.
junior year is usually when you are 16 to 17, same dependance...
though you might have not notice the part where they FIRST attempted sex when juniors... then it was at least a month before they tried again, who knows how long it took to get to the groove spot they mention for time number 5...
then 10 months later, they split up.
so if it were a few months between try 1, and try 5, zach could easily have already started college...

To go further, they make reference to them both being genius', so it is possible that zach graduated a semester early, thats not even hard to believe. it happens quite a bit.
he could have then gained early admission to college, or even just started with summer classes. no, it is not what most people do, but i know quite a few who do.

so the time line works easily enough without him getting out of high school a little early, and into college a little early... but if you do allow for that, it more than works.

To answer the question you are wrong. It does not have a major plot hole. If they had summer birthdays then it would fit. I was 15 my entire sophomore year. My niece is a late summer birthday and she won't turn 18 until a week before she starts college in a few years. Also most wouldn't be that age there junior year like you say. Since the four biggest months when babies are born in the U.S. is the summer. Three of those months are when school is out.

I was 15 when I started my Junior year. I have a late birthday and started school when the cut-off rules were different from what they are now. I think I'm close in age to what the characters were supposed to be.