What would cause this weird bearing wear?

I took off a few caps to re-position them a bit, and now they are flush with one side and nice and straight now (could only adjust the movement front and back) torqued everything down and crank spins nicely still. Is there anyway to ensure that everything is in the right place? For all I know they were good before. All I did was take a cap off and re-position, didn't move the crank at all, I also didn't touch the thrust bearing as it was perfectly lined up.

Also they may be fine but Ive torqued these stock main bolts a few times now, can I replace them with some new stock bolts? Not arp because as I understand the extra clamping impacts the cap. Can you even buy the stock ones?