Factual error: House is playing 'Metroid: Zero Mission' on his Gameboy at various times. The Metroid series does not feature space monkeys, nor are there distinct levels. The sounds coming from the game in the show do not match it in real life, and Samus morphing into a ball is most definitely not a failure state.
Factual error: In episode 414, "Living the Dream," the patient Evan is given a nerve function test. We see Kutner and Taub performing the test by puncturing Evan's legs with needles. Modern nerve function tests actually rely on electrical impulses from a small computerized device, with no needles necessary.
Factual error: When House is looking over his whiteboard of symptoms for the swimming patient, the symptom "Intercranial Hemorrhage" is shown on the board. However, this is an error. The correct term is "Intracranial Hemorrhage." Anything inside the head is referred to as "intra" not "inter." This is a common mistake for laypeople, however the highly trained and knowledgeable Dr. House should not have made that error.
Factual error: A kid is being taken to surgery to remove a magnet he swallowed because it may be stuck in his upper intestine. House diagnoses that the magnet is already in the lower intestine by taking a scalpel and showing that it's magnetically attracted to the lower abdomen. Surgical scalpels are made of high grade stainless steel and are not attracted by magnets.
Factual error: There are several episodes where doctors continue to defibrillate a patient even after s/he flatlines. A flatline (asystole, where there is no electrical activity in the heart) cannot be corrected by defibrillation, which stops a heart that's in an abnormal rhythm and gives it a chance to start in a normal one (the heart has already stopped when there is a flatline).
Factual error: The boy plays a game of chess at a tournament against some other person. The camera only shows a few pictures of the board, however, when the boy says "goodbye" and the game ends, due to an allegedly checkmate, the following is shown: the opponents king is on f7, with his own figures all around but e8 and h7-9 being free. On h5 is the boy's rook which attacks the h7, h8 and h9 fields. Now the boy moves his bishop to h6, thus attacks f7 (where the king is) and e8 (the only free spot but h6-8). Now of course h6, f7 and e8 are not available to the king anymore, but as the bishop blocks the rooks attack on the h-line, the king now has the fields h7 and h8 to go to. Thus it's by no means "checkmate."