Are the lenses soft or hard/gas permeable ? I wonder if what has happened isn't that your cornea has been damaged as you took out the lens and that is what gives rise to the pain - the likeliest cause being lack of cushioning by the moisture normally in the eye. Another possibility is a poor fit, the curvature not being appropriate. I have had this sort of thing happen very occasionally, not very severe but still there. In my case it has been most likely to occur the longer it was since I last used the lenses, and then after wearing them for many hours first time again.