I sealed garage windows with rope caulk but I still feel too much heat is loss through the glass, is it a good idea to cut out a 2'' rigid foam to the dimensions of the window sills and cover it? The window is facing north so it's not receiving much sunlight during the time. I leave the foam board off during the time and after I come home at night I will put it up on the window frame. I just want to know if this will cause any harm to the glass of the window.

Adding insulation to the inside of the window frame should not cause any harm to the glass. It may cause condensation on the inside of the windows if the absolute humidity in the garage is higher than the outdoor humidity. If the window frames are vinyl, then any condensation should not be an issue anyway. If the frames are wood, then it would be useful to check for condensation.

Thanks, I found the following to be useful: http://www.builditsolar.com/Projects/Conservation/EdgeSealsShurcliff.pdf