If you have contact lenses, of course you can wear them instead of a pair of frame glasses. 3D glasses can be easily worn with contacts.So there is no need to worry about it at all.
It’s a good question cause today there are so many 3D movies. Actually the theaters also notice the issue and they invent the clip on device. You can just put on a clip on your glasses and you are able to enjoy the movie.
One simple solution to wearing 3D glasses with regular glasses is to wear them on top. This can be a bit uncomfortable, but is certainly the easiest solution to the problem.