As for the practice itself, think of the following situation:
You are a Comcast TV customer and you just signed up for their internet. THey did not provide internet for the first month so you don't pay the internet bill. Does this give you the right to not pay the TV bill because they breached the internet one?

Without a contract you're going to have a hard time showing anything. But they have to pay for what they agreed to, your dispute on project B is an entirely different matter, especially if you've delivered the files. If they don't pay project A in full, don't give them a thing.

This is why it is important to have a contract that outlines how this stuff goes.