I tend to use canon characters, but yes, that has indeed happened to me. I think it's because I don't plan things out beforehand, so I just write in whatever direction I think it the easiest.
Often times, I might have a certain intention in mind. I may have a general idea of how I want to portray a certain character, but after I finish things up and read it over, I'll be like, "Whoa!" because I've just realized that my character has turned into something completely different from what I would have expected. Things can get out of control when characters take over; sometimes it's a little inevitable, it seems.
I've also written original fiction with characters of my own creation, so in my head, I've developed them and I know what their personalities are like. But when I insert them into the story, they often surprise me by doing things that I would have never imagined.