I had that problem also, after I upgraded my RAM. I thought the screw hole was striped & just 'thought oh well...', & left it. After reapplying the thermal paste i tested the screw hole without the bottom cover & it looked like it was good. I think the holes on my bottom cover are off just a little (but the screws were flush before so I it must fit).
I advise you to tighten each screw only about two turns each until they're all in place. Then going in a circle, screw them all in until you get some resistance. Finally, go in a circle again screwing them until they're all tightened up.