this is pretty odd. i had one in our "spare room" and it sat on the carpet. never wanted to ine up or anything and the door was just like this... well i eventually mover it to a solid floor and secured it to the floor. never had any other problems with it. were the ones you looked at sitting on the concrete floor? that's not good!
I think the ones in the Tractor Supply store were still mounted on their thin shipping crate metal. So maybe it's just slight bent or twisted.
But I just stopped in Dicks again, to pick something else up, but decided to go take another look at the safes now that I know how to spot their dial combinations. And I didn't see anything inside of the safe that would allow for adjustments to make the door seal tighter. And those were directly on the floor. Which is a pretty solid floor. But still up on the second level.