I like to think not haha
never had this problem in lets say 3d land when the 3d was on.
The problem I think is the camera and even some of the levels seem designed as if you were viewing it in 3d. This probably why I'm quite good at games like sunshine or galaxy but 3d world can end up with me dying because I thought I was going to land somewhere I wasn't.
I played it on a 3d tv and it really does help.