I have always had trouble mounting small hardware on small wood boxes, with the hasps and hinges always looking slightly off perfectly square - particularly a problem with flat head screws and countersunk hardware which aligns the hardware to the hole location and centers on the hole.

I'm talking small wood screws. I place and mark the hardware carefully and mark the center of the hole with a sharp awl.
The problem comes about with small bits like 1/16 and 5/64 and 3/32"...