Continuity mistake: When Alejandro finds Maya outside the tunnel, she has black ooze from her eyes running down her cheeks. As he starts his healing, we get a close-up shot of how the ooze fades and disappears from Maya's face. But in the next shot of her face, when she falls forward, the black stuff is back on her cheeks. It's gone again in the next shot of her.
Continuity mistake: Season 2, ep. 3, "Kindred". When Peter gets the box with his belongings back from the Irishmen, as Caitlin says "Well?" Peter's hands are in his lap. The angle changes to Peter, who answers "Well, what?" and he suddenly has both hands on the box, with no time to move them between shots.
Continuity mistake: When Maya is arrested, she starts manifesting her powers on the policeman. In a close-up, we can see the black ooze coming out of her eyes. Cut to a shot from above, when the policeman's eyes turn black and he drops the handcuffs, and Maya's cheeks are suddenly clean again, with no trace of the black stuff.
Visible crew/equipment: When Claire runs away from Bob after he calls her "Ms. Bennet", you can see Bob's shadow and another person's shadow on the ground. Since no one else was standing next to them, it has to be a crew member, most likely a camera man based on the odd shape of the shadow.
Continuity mistake: Season 2, episode 10, "Truth and Consequences": In the previous episode, "Cautionary Tales", when Noah was brought back to life he regenerated, then sat up, looked around him and said something sounding like "Home". In this episode, when the exact same scene is shown, we see Noah regenerating and sitting up, but this time he just looks straight ahead before lying back down, and does not say anything.
Continuity mistake: Season 2, episode 11, "Powerless":. In Mohinder's kitchen, when Sylar cocks the hammer of the gun he is holding on Mohinder, he is holding the gun with his arm straight and the gun completely level. The angle changes just as Sylar says "Maya, I need you to stay calm", and now his arm is close to his body and bent so the gun is pointing at Mohinder at an upwards angle. There was no time for him to move his arm in between shots.