I've run into the same problem. I think crates might have a maximum capacity in the game (maybe not in the editor, but in the game). So if the crate is "full" you cannot add more stuff to it. This same thing happens with vehicles. Once they are full you can't put any more weapons or ammo in them. Also, if the vehicle is almost full, but still has room for, say, your M16. You can put your M16 in the vehicle but the magazines end up on the ground (if your lucky, because sometimes they just dissapear).