When Sam crawls into the cannon on the topdeck, he enters head first. When he comes out, he's facing in the opposite direction.
In the sequence where Bugs is running from door to door on both the upper and lower decks, all the doors have knobs on the left-hand side. When Bugs runs out of and back into the right-hand door on the lower deck, there is a cut to a closeup where Yosemite Sam opens the door to find a canon aimed at him. The door he opens has the knob on the right-hand side.
The first time Sam tries to bring Bugs down from the combination crow's nest/elevator, he presses the "UP" button and brings it down.
When Sam fires his pistol at Bugs, he somehow is able to fire three times in rapid succession - from a single-shot pistol.
When Sam climbs the rope and goes over the pulley, he should never have gotten off the deck, since the other end of the rope is not secured to anything. Thus, there is nothing to counterbalance Sam as he climbs the rope.
When Bugs drops the anvil on Sam, and Sam catches it, the ship sinks to the bottom. When Sam tosses the anvil overboard (under water), the ship floats again. If the weight of the anvil made the ship sink, it should have been on the bottom when Bugs had the anvil in the Crow's Nest.
When the crow's nest is first seen, it has the misspelled phrase "CROWS NEST" (no apostrophe) on the side.