Hi. There is a problem though. If I go for legal advice like employment act in Canada or contact representative in town. At the end, it will be my former PhD supervisor pay me out of his own funding for that ~ $ 2000 - 3000. I do need his reference letter in the future. Although we had a good term and he mentioned will support me anything, but I am not sure if this is about money...

Will he hate me if I ask for money and not give me reference in future?[/quote]

That's the risk you run. Technically your supervisor should give you a fair reference, but that doesn't mean he will.

Have you tried asking him straight for the money? Like "I've had to pay back to my stipend, but I worked for you in good faith, and I'd like to be paid for that..."?