Visible crew/equipment: In the final fight scene on top of the submarine you can see the ripples and shadows on the painted sky backdrop behind the submarine. (01:31:05)
Revealing mistake: When Robin is trying to get the sub to surface using Bat Depth Charges, the sub is rocking violently. The rack that contains the vials with the Security Council's dust not only sways back and forth, but lies nearly flat several times, and always at impossible angles. This goes against physics, and gravity. The rack should have fallen off the table more than a few times.
Other mistake: When searching the buoy for clues, Batman goes to take out an obvious screw that was supposed to hold on the panel hiding the projector. The screw is located in the top of a seam where two panels were riveted. After removal, the panel is removed and you can see the seam again that would have been hidden by the panel, as it was tall enough to fit the side from the walkway to the top. Also, the lenses on the projector were obviously fake. Any projector with lenses that badly chipped and faded would have been repaired or replaced. In addition, Batman is supposedly loosening the screw, but was turning the screw to the right, which would be tightening it.