The same thing happened to me two years ago in Ticino. My old school had an agreement saying I didn't need a visa. My new one did. Never knew about it until I was trying to get my permit. Soooo, I basically went to the police and filed a report of what happened. Admittingly I entered the country illegal, but not intentionally and I was led on false information to do so. The local prosecutor declined to press charges and with that letter from the prosecutor I was allowed to receive the permit.