Nuke disk duplicates itself on disk respawn.

[UrsulaMejor]

In most cases disk duplication is intended. The issue in the past was captains leaving the z-level and noticing the disk mysteriously vanishing from their pockets, followed by promptly screaming "NUUUUKE" and scrambling to reaquire the disk and bunker up.

This is presumably related to that.

the problem with this explanation is that it's clearly not intended; duplicate disks can't be used in the nuke properly and also break the pinpointers