Plot hole: If Noah could be brought back from the dead with Claire's blood why couldn't they bring back Nathan? Was turning Sylar into Nathan really the first thing they could think of?
One of Us, One of Them - S3-E3
Revealing mistake: When Tracey looks at Nikki's dead body in the coffin (both played by Ali Larter) we can see Nikki's eyelids flicker.
Our Father - S3-E12
Continuity mistake: "Our Father". At the end of the previous episode, "The Eclipse, Part 2", Hiro brought Claire to the rooftop of the Deveaux building to witness Kaito handing over baby Claire to Noah Bennet. To illustrate his point, Hiro showed Claire the exact same thing happening in the "9th wonder" comic book he brought with him, and she can follow the Japanese dialogue from there. But when the exact same scene is shown at the beginning of this episode, Hiro does not show Claire the comic at all.
Other mistake: Peter rescues Angela from an elevator by flying her straight up the elevator shaft. When we see the shaft, it is completely devoid of any elevator cables.
Visible crew/equipment: When Daphne meets Linderman at pine hurst she walks to greet him and you can see a crew member behind a tree on the right side of the screen. (00:42:05)
Continuity mistake: When Sylar is impersonating Nathan, the knot on his tie keeps changing between scenes.
One of Us, One of Them - S3-E3
Factual error: When Hiro and Ando stand in front of a cinema in Berlin, Germany, you can see three movies posters in the background announcing a Buster Keaton festival. The left one shows his movie 'Cops' - but the German title 'Politzisten' is wrong - it should be 'Polizisten'. (00:09:55)
Continuity mistake: When Claire Bennett is cutting Peter Petrelli's chest she makes two cuts then the angle changes and the blood is gone, the angle changes again and it is back.
Continuity mistake: When Claire is looking at the "Alice in Wonderland" dust jacket, she holds in one hand looking at the back cover, then in the next shot, she's holding it with both hands looking at the front cover. (00:24:40)
Chosen answer: Hiro's powers are still quite unreliable, and a locked closet door isn't a huge obstacle. Since Hiro knows he needs to rescue Ando, it's probably safer to try and bash the door down than risk teleporting to the wrong place or time.