My son is 2 and was prescribed amoxicillin for an ear infection. is it possible that the antibiotic is causing him to have nightmares?

I've never seen it: I've never had it reported in > 3 decades of practice. On the other hand, the discomfort of an ear infection often leads to sleep issues that improve as the kid improves. Picture you trying to sleep if you have a tooth ache, you may be able to fall asleep if exhausted but will likely have difficulty settling most of the time.