Update!
I think that the save is broken or something. Other containers loot started respawning around the map for example the Riverside gas station and the Giga mart in West Point.
We managed to recreate the bug in the gunshop and it isn't to do with my friend it happens every 2-5mins automaticly even when we are away from the gunshop, so we are now thinking that the save is broken.
We had the thought to burn the building down to stop the bug.