Plot hole: When the fat guy throws a boot into the ice-spray room, it freezes and shatters on the ground. You can see the length of the shoelace on the ground as well. The shot cuts to the guy in the shaft, and he pulls up the shoelace to reveal the end encased in ice, while the end is halfway into the ice block. This wouldn't be possible, because the other end of the shoelace had no ice at all, and there's no sign either of it breaking.
Plot hole: The tunnel at the base of the stairs under the church wasn't connected to the stairs and seems to only have been reachable with the elevator system.
Plot hole: The plot that a piece of the Roman spear that pierced Christ ends up in a hidden Mayan temple in the Amazon (which is nevertheless still full of gold etc.) makes no sense.