Can a bank hold the title to my car after its been paid off because I have a negative balance in my checking account with that bank?

Your lender and bank can refuse to transfer legal title to the vehicle that you had a loan for which has been paid off because you have a negative balance in your checking account. However, for the bank to do such is improper. The dispute with the checking account has nothing to do with you getting legal title for the car that you paid off.

I suggest that you have a face to face meeting with the bank's manager to get the matter resolved and registration to the vehicle in your name.