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.
Continuity mistake: Charlie, Olivia's former partner and friend in the FBI shows up in this episode during the interview with Mrs. Rusk, but Charlie was killed off by one of the shapeshifters in a previous episode, and the shapeshifter that killed Charlie was himself killed off by Olivia, who in other episodes reflected back on killing him.
Continuity mistake: At the very end of the episode when Nina Sharp exits the elevator, she mostly steps out of the elevator completely before the masked men come and shoot her. However, when they review the security footage of the attack in the next episode, "There's More than One of Everything," you see that she barely takes a step before being shot.
Revealing mistake: When the typewriter is being used at the end, the keys being pressed don't correspond to the words appearing on the paper. Obvious from the start - the first letter pressed is on the middle row of the keyboard, but the first word typed is "unacceptable".
Character mistake: When Walter is saying his father was a scientific pioneer at the university of Berlin, Peter reacts by saying: "Yeah, I know. Who came here in 1933, which is long before the Nazi's ever took power." In fact it is EXACTLY when the Nazi's took power: 30 January 1933.