When Peter disappears after talking to Claire, the branches on the tree behind him shift dramatically, giving away the cut.
When Peter flies in to save Claire from the oncoming train, he clearly has the floppy hair style from the first season of 'Heroes', which then changes to his newer style when they both land
When Mohinder rips off Maya's blouse, a light brown modesty garment covering her breasts and midriff can be briefly seen as he spins her around. Previous shots establish that she is not wearing anything under the blouse.
When Hiro explains to Ando that he's hired private detectives, the subtitles read "Very discrete." A common error. Discrete means separate. They should have written "discreet."
While walking through the desert, Parkman walks past a vulture on a log. The straps holding the vulture to the log can be seen on its feet.
When Mohinder demonstrates his newfound powers to Maya by climbing up the wall, the lights hanging from the ceiling by metal poles oscillate in such a way that reveals them to be mounted perpendicular to the force of gravity. This gives away the fact that Mohinder is actually scaling a set designed to look like a wall.