When I was younger, the place I was working at did this. Come T4 time, what they paid me and what they reported were two different things.
The first step I took was to get them to correct this issue... no luck. I did this in writing. This is important.
My next step was to write the CRA Enforcement branch and share my concerns. You'll be surprised how quickly you will get a response. Drop this off at a CRA location and time stamp it OR send it registered.
Anyhow, CRA made me file my return with the information provided on the T4. Over the coming months, I had numerous people asking for copies of pay stubs. Eventually my return was adjusted accordingly to what I owed, and excess taxes paid refunded + interest.
I quit after they wouldn't amend the T4... as I heard from one my old co-workers, CRA showed up with the Police to confiscate almost every piece of paper.
The short of it, CRA is very powerful monster... don't get caught in its jaws. If you paid extra money on your taxes, don't sweat it, you will get it back. Just be sure to keep good records and be honest with them.
The fact is, this smells fishy and you need to CYA.