Continuity mistake: When Jack speaks to Michael and Jin, as they build the raft, and then when he walks up the beach and inquires about Sawyer's trouble with his head, the backpack that Jack carries on his back is nylon, black/green with white trim. Yet, when Sawyer asks, "Sensitivity to light, that bad?" the backpack is suddenly transformed into solid black leather, of an entirely different style. Then, in following shots it jumps back and forth. (00:16:40)
Continuity mistake: When Jax and his crew meet up with a Hispanic gang to sell them guns and are outnumbered, they run in the station wagon. The run the station wagon through a gate and roll it, destroying the front end, but magically the station wagon's front end appears with little damage afterwards. (00:27:15)
Plot hole: The very ending scene where Peter (in this version died in the ice as a boy so Walter's wife never met him) takes off some of the dust covers then picks up a toy airplane. The toy airplane he got as a child from ... Walter's wife when she was trying to placate him in an earlier episode for trying to run "home". This toy airplane wouldn't have been his as a child in this version of the universe. (00:42:00)
Continuity mistake: In this episode, Booth and Bones are telling Sweets about their "real first case" together - the case where they actually met for the first time. During this episode, Booth, Bones, and Angela take some evidence to Caroline, and Booth introduces them both (most importantly Brennan) to Caroline. However, in season 1, episode 19, "The Man in the Morgue", (which would have taken place after this initial first meeting) when Brennan is accused of murder in New Orleans, Booth has Caroline fly to NOLA to be Brennan's lawyer, and he introduces the two of them. If they had already been introduced during the first case Booth and Brennan worked on together, they would not have needed to be introduced here; they would have already known one another.
Continuity mistake: When the two factions of Hondo's pirates are fighting each other, the ones who sided with Maul and Savage are using blasters that fire red bolts, while the ones that stuck with Hondo shoot blue bolts. When Hondo persuades the traitors to work for him again and they attack the two Sith, all of the pirates' blasters are now firing blue bolts. This is Star Wars, not G.I. Joe, and weapons don't just change colour like that.