I haven't read the other responses yet, but this is how we handle situtations like that where I work (fooling around in the bathroom, like the principal said)- those two students would not be going to the bathroom at the same time (heck, I do that with a lot of the kids anyway just to stop fooling around). And, if it were more serious than fooling around, the "guilty" student either uses the nurses bathroom or, if the principal is available, he goe with him. Again, the student isn't denied using the bathroom.
As for the way the teacher spoke to you, I would talk to the principal. Not in the "my kid can do no wrong" way, but about the tone and attitude of the teacher. Also tell the principal you are confused because he said it was a one time thing, and the teacher said it was the third time. It's possible there has been other incidents of fooling around that the principal wasn'ttold about at the time. But, if I were the teacher, when I reported the last one to him, I would have made him aware of the other two as well.