The Ontario government web page tells you how to go to City Hall or a Municipal Office and get a marriage license. However, it doesn't say you can go to whatever municipality you feel like, nor does it tell you how to choose.
If a couple are both living in City A, and the ceremony will be in City B, must they get their license from A or B? Does it matter? If they both work in C and it's easier to stop by the C offices at lunchtime, is that OK? Or could there be a problem if the certificate was issued by the "wrong" municipality?