Plot hole: We see Hogan's men empty out the gunpowder from a lot of cartridges inside the armoury. What did they do with their empties? It's not like a mound of empty cartridge cases on the ground wouldn't draw some suspicion is it? Yes, I am aware some options come to mind, e.g. putting the bullets back in and stuffing them back into the belts, but none of that is actually shown or talked about - LeBeau even chucks one cartridge over his shoulder, implying they are not very concerned about hiding their tracks.
Continuity mistake: During his experiments to create explosives in the tunnels, Carter has a pretty extensive set of glassware on his workbench. Necessarily he would have to replace (most of) that after each explosion - not to mention various light bulbs, furniture and other non-blast-proof stuff by the way. A lot of that glassware is specialty equipment, it would not be easy to come by even one set of in peacetime for a free civilian. In wartime, for an allied prisoner (even with the heroes' connections) it should be nigh impossible, and totally impossible to have an inexhaustible supply of the stuff. So we can either assume a giant plot hole, or treat it (as I did) as a big continuity mistake.