Most likely some error arose during the year. If possible go back and see where /if they ever matched . If you are paid monthly it shouldn't take that long. Once you find the time that ut differs ask your payroll if the error was on their side or revenue.
Getting and answer from revenue is time consuming 3 months in our case, and 9 months to admit they screwed up, lost return a few years ago but they took exact amount from bank.
I would do the return based on what you actually know is correct not what they say, but write a letter. If they are wrong they will correct it, but you need to be very specific on where, when the figures differ.
I would do it that way, others might have other ways .