Revealing mistake: When the shark is on the deck of the Andrea Gail, you can see the equipment underneath it that is making it move. (00:47:30)
Revealing mistake: When Capt. Billy Tyne climbs up the boom to free the loose anchor, instead of a real flame on his cutting torch, there is what appears to be a piece of illuminated glass.
Revealing mistake: Towards the end when the boat is going up the huge wave, notice Billy and Bobby are keeping their balance although the boat is straight up and down.
Revealing mistake: When the men are trying to put the plywood on the windows, one of the men gets blown off the boat while holding the plywood. Just before the scene cuts, you can see the harness and wire on the back of the stuntman.
Answer: Not a ship captain, but will take a shot. If a massive wave is close to cresting, as I seem to recall in this scene, the boat would have to climb a near vertical wall of water and would likely be flipped back and upside down by the advancing wave. Perhaps he was planning to gun the engine to penetrate the wall of the wave, and bob to the surface after it passed. Reversing the engine would just let the thousands of tons of water in the breaking wave smash down on the boat, crushing it.