Should teeth have to be filed down after Invisalign to make the bite fit?

I just finished my treatment and after going in to see the dentist, she removed the buttons and cut off the last 2 teeth off my last tray, however, my teeth do not line up and i cannot close my bite. Is this normal? will my teeth actually "settle" in place or should i be asking for additional trays to fix this? I feel like my dentist didn't really even check my bite to see if it was correct. It seems like a lot of money to have to file down my teeth to fit?