Water pump kit from LMR doesn't look right..

I was laying under the car today trying to get some wiring done and I noticed the water pump bolt is touching the timing cover and not allowing it to seal! Good thing I didn't find that the hard way but what could I have done wrong? Is the hardware that LMR provides incorrect?? I'll have to replace that bolt with a button head I guess.

I found some better bolts, replaced them, and now I'm pretty sure the timing cover is warped. I took it back off and checked the cover and pump with a straight edge, the pump has quite a bend to it and the timing cover seems ok with maybe a 32nd gap at the bottom.. time to order another new pump and try again. I hope someone learns from this! I would've never thought that the pump could bend.