Changing from knob to lever or from one handleset to another. Rose and escutcheon sizes vary, so the new trim may not cover what the old one did.
Changing from a mortise lock to a tubular lock. Older doors often have a deep mortise pocket cut into the edge for a box lock. A tubular latch needs only a small bore, leaving most of the pocket empty.
Moving the deadbolt. A deadbolt moved higher or lower on the door leaves the original bore behind.
Removing a lock altogether. Surface bolts, chains, a second deadbolt added after a break-in, or a keypad that has been taken off all leave holes.
Previous repairs. Doors that have had several locks over the decades can carry three or four generations of holes, some filled and some not.