Well, as the OP is the last out and first in, and the alarm hasn't been tripped, it doesn't smell like theft to me. I worked retail for a long time, and I saw my fair share of theft- internal and external. I'm more of a mind to bend towards equipment or predation. I do think, that a night of video surveillance after the minnows come in would help determine exactly what's going on.
You are sadly right though Charrr89- people do the stupidest things, like stealing bags. Pathetic, and why would you risk your job to do something like that, and yet it happens.