I think something doesn't quite add up here, are you sure you're not making it up as you go...?
Firstly, the visa-waiver program (VWP) only works for citizens of certain countries to enter the USA. Poland is not even on that list of participating countries, so you're wrong straight off the blocks.
Secondly, US citizens can enter Poland (or the whole Schengen area) for 90 days in any 180 day period without a visa. Going out (even if you actually went out of the Schengen area, which going to Berlin does not qualify!) every 90 days for a short while and returning for another 90 days is straight away a visa violation.
Thirdly, 'receipts for trips' is hardly proof of having left the country. And given that there are no border controls within the Schengen area, you couldn't get your passport stamped with exit and entry stamps even if you wanted to.
Fourthly, I very much doubt that the Polish immigration or border control authorities would say things are 'fine' when you call them. Things clearly are not fine, and even if they were they wouldn't say so on the phone without getting more details first. Besides, I'm assuming you didn't record those phone calls, so how would you ever prove that someone said that to you?
Fifthly, I don't believe your university would have allowed you to enrol without checking your visa status, as they are likely to get major sanctions for allowing illegal students to study there.
Sixthly, if you're so dumb that you are basing your study arrangements on hear-say about some vague visa-waiver arrangement without bothering to look into it a bit more, let alone without realising that such waivers are obviously only ever intended for short leisure or business visits and not for staying for years on end, then I'm pretty sure you're not clever enough to have been accepted into any medical school anywhere!
Ergo, the whole story is clearly BS.