The blunder came to light last night and the Financial Regulator has been informed.
A statement from AIB said: "The error happened when customers were charged an interest rate that did not match the loan-to-value ratio on their account."
The bank said that it offered different tracker interest rates to its customers based on the size of their mortgage compared to the value of their home.
It also admitted that "in some instances a 'new business' discount was not appropriately applied".
Two years ago, AIB refunded more than €250,000 to 3,700 customers after it mistakenly charged them for stamp duty on their credit cards.
The AIB overcharging comes hard on the heels of a Laser card glitch at Bank of Ireland which double-charged up to 200,000 customers.
Bank of Ireland customers who used their Laser cards last Friday found their accounts were mistakenly debited twice each time they used the card.
Many ended up with their accounts overdrawn in the next few days because of the error.
A spokeswoman for the regulator said the Consumer Protection Code required that firms speedily, efficiently and fairly correct charging errors and notify affected customers.