I haven't experienced that with games but if I spend an hour or more taking lots of photographs with an SLR camera, one of my eyes sometimes ends up out of focus for a while from squinting into the viewfinder.
Slightly off-topic but I've also noticed that if you wear 3D anaglyph (red/cyan) glasses for a long time, your brain (knowing that the colour information from each eye should be the same) actually starts to 'correct' the colours. When you take off the glasses, your view through the eye that had the blue filter in front of it has a red cast and vice versa with the other eye. So I guess if you spent some time wearing the glasses upside down, when you took them off you might be able to see anaglyph images in 3d with the naked eye for a while. I don't recommend trying it though.
Slightly off-topic but I've also noticed that if you wear 3D anaglyph (red/cyan) glasses for a long time, your brain (knowing that the colour information from each eye should be the same) actually starts to 'correct' the colours. When you take off the glasses, your view through the eye that had the blue filter in front of it has a red cast and vice versa with the other eye. So I guess if you spent some time wearing the glasses upside down, when you took them off you might be able to see anaglyph images in 3d with the naked eye for a while. I don't recommend trying it though.