Continuity mistake: After the interrogation, Skye tells Agent Coulson about Agent Ward. Coulson says during this scene,"It's a magical place" and Skye says "Ward doesn't like your style. Kinda think I do." At the end of this line, Skye is looking at Coulson. In the next shot, she's suddenly looking 90 degrees in the opposite direction.
Continuity mistake: In the scene when Coulson is using a diagram to explain to the team that Cybertek is the common denominator of everything that's happened during the season, he starts tracing lines that connect various bubbles of the diagram to each other, ending with one that links "the bus" to "GH-325." In the next few shots that last segment suddenly disappears, only to reappear later on.
Continuity mistake: When Coulson, Ward and Hill are watching the video of Mike saving the woman from the burning building, as the shot cuts to Coulson saying "A little present from Rising Tide", there is a long reflection of his watch coming from a light. Coulson doesn't move in the next shot. But the reflection has gone when the shot cuts back to him.
Continuity mistake: In the opening scene where Mike and his kid have a conversation outside a toy store, an explosion comes from the top floor of an apartment building. Just before Mike runs off to go save some of the people from the building, he says "Stay with Bernie" to his kid and Bernie then does this. After he says this and runs off, the kid and Bernie are a good foot away from the toy store. The next shot when Mike shouts "Watch my boy!" to Bernie, the kid and Bernie are a great distance away from the toy store without any time to move.