When Mohinder is in the secret space in Sylar's apartment, in the shot from behind where he is looking at the writing on the wall, he is suddenly wearing a brown jacket and his camera strap disappears.
When Suresh finds the key in his father's book, the length of tape on the key varies between shots.
When Isaac is going through his sketchbook he goes over the same page in different shots.
When Peter is telling Simone he is quitting, a fire truck marked "Los Angeles" is visible through the lobby doors. The scene is set in New York.
When Hiro first shows Ando the comic book from the future, he tries to prove the comic's authenticity by pointing out that the dialogue of Ando in the story matches what Ando says in real life. However, the comic book is written entirely in English. There is no explanation for how Hiro (who barely understands English) could know that Ando's words (spoken in Japanese) match those in the book.