Plot hole: Shortly after the ship flips over, the steward, Acres, is asked why lights are on. He explains they are emergency lights that will last three hours. The lights are left on throughout the movie, but when they get out it is bright daylight. Considering the ship flipped at midnight, there is nowhere on any ocean where it gets light at 3:00 in the morning.
Plot hole: When Michael is punched, the Don has just been shot and is near death. A gang war ensues and progresses. The Don recovers enough to be brought home. Michael moves to Italy, meets, courts, and marries his girl. Sonny is killed. Michael's wife learns to drive and is assassinated - and still, Michael has very visible remains of his black eye. Way too much time must have passed for this to be possible.
Plot hole: When in the woods, Mari's friend asks to put her clothes on. The man says that its OK, yet Mari puts on her clothes too, even though the man said that only the other girl could.
Plot hole: Shaft's friend has been killed at the beginning of the movie. Bad guys show up at his sister's door for a fake flower delivery, and Shaft kills them. He asks the dying baddie "Who put a contract out on me?", but how does he know? We as audience know there is indeed a contract on Shaft since we've seen the conversation with the mobster, but as far as Shaft knows, all evidence points at Arna being the target, and he even explained the money-related motive a mere minute before.