The 3D glasses adopt the special material to let you see the screen like in the same situation. If you feel light headache, there may be some reasons to explain it. First of all, you don't wear in the right position which causes your eyes not see properly. Secondly, the 3D glasses are too big and heavy for you to wear, which could also make you feel headache.
Well, it is normal for many people to be in this kind of situation. In my opinion, you are not familiar with the 3d glasses which are different with the normal glasses. So when you wear them in the first time, it will just make you feel not so well. But I think if you try those more often, this uncomfortable feeling will just disappear. Besides, even you have tried those many times, you still can not be accustomed to them, maybe you should not wear them and have a test on your eyes. So that you can make sure what happened to them.
Well, as a matter of fact. People, I mean, every one of us are used to normal vision or glasses. When your eyes are exposed to something unusual like 3d glasses which are especially deigned for 3d experiences, we might get dizzy, get a headache, even throw up, since you are not used to that. Apparently, that is caused by wearing 3d glasses. However, as time goes by, that feeling will be relieved.