My son has epilepsy. He's been having minute to 2 minute long breakthrough seizures. Had a 2 minute one today after med change. Any idea why?

Depends. Unlike an infection, which after culture, we know what antibiotics to prescribe, we do not have that specific a test. We learn about the adequacy of an anti seizure medication by its effect. It may take several days for any change in medication to reach a new blood level plateau, so it may take time for a change to be effective.
Transitional events. The declining level of any anti-convulsant is a prime reason for recurrent seizures.If your kid had some level of benefit from the one you stopped & the other med had not reached protective levels yet, breakthrough would be a possibility. It is not uncommon to go through several meds before finding the one or combination that gives the most benefit.
Medication Change. Hard to say for sure without having seen him, but if he recently had a medication change and now his seizure pattern is different, then the medication change would have to be at the top of my list of causes. Definitely need to talk/follow up with his physician.