Revealing mistake: When Ripley is leaving New York, there is the shot of the ship sailing out of the harbour. Check out the water - one layer has been 'cloned' on top of another.
Revealing mistake: During the scene on the boat while Ripley is reading the book, Paltrow gets out of the water and walks to where she is leaving a trail of wet footprints. If you notice there is already one set of footprints that have not dried from an earlier take.
Revealing mistake: The letter which is typed on the Olivetti portable typewriter (certainly an accurate model for this period) is obviously a modern laser-printed letter, not from a manual typewriter.
Answer: After running into Meredith, Tom's plan was to stay in the cabin with Peter the entire trip to avoid them seeing one another. But after Tom makes that suggestion, Peter tells Tom that he seen him kissing Meredith. He couldn't avoid or kill her since Peter already saw her. Family members also saw Tom with Meredith. If Meredith suddenly vanished or was killed I'm quite sure there'd be an investigation. Peter was the only option. No one is on board to report Peter missing. Once the boat docks, Tom will be long gone before they discover Peters body. Unlike Meredith, her family would be looking for her immediately since they're traveling together. I'm quite sure he'd much rather have killed Meredith, she meant nothing to him.