^ What they said.
When your eyes are exposed to that kind of thing for too long, the parts of your eyes that pick up the red and blue colors respectively get fatigued, so when you take off your glasses, you see the "negative" (inverse or opposite) of that color. The inverse of red is blue, and the inverse of blue is red. So when your eye is exposed for red for a period of time, when you take the red away, you see blue - and vice versa. That's why you're seeing the colors in reverse.
As the others said, it should go away after a while, but it really is not healthy for your eyes to be wearing the 3D glasses for prolonged periods of time.