The putty knife catching on the screws could just be due to the shape of the screw head. Typical pan-head screws are chamfered slightly on the bottom of the head.
Cracking the skylight from (apparently) over-tightening the screws is not normal, or at least not proper. It sounds like it may be a good idea to put a flat washer underneath the screw when you do your repair to spread the stresses out some more (or alternately use a screw with a bigger head, such as a lathing screw, but I think the washers would be preferable in this case). If you can find some sort of stiff but flexible washer (nylon or something), that may be even better.