Continuity mistake: After Sarah finds her father in the bedroom and goes downstairs to get help, the blood pattern on her shirt/upper breasts changes. While the movie is edited to look like one continuous shot, it was filmed in bits and pieces, and the blood pattern was not consistent in some of the shots, it seems.
Factual error: Colonel Meyer's promotions are listed in his SS ID card as Hauptmann, Oberstleutnant and Oberst. Since the SS used a different ranking system from the Wehrmacht, they should actually be Hauptsturmführer, Obersturmbannführer and Standartenführer.
Revealing mistake: As the guy is being pinned down by the giant hooks you can see for over a minute he can simply escape and slip his hands out. (00:52:30 - 00:53:30)
Factual error: In his crude attempt to replicate the Human Centipede surgical procedure, Martin employs several handyman tools, including a carpenter's staple gun (using T50 staples as sutures). Problem is, carpenter's staples would never join soft human body tissues, they'd pull right out with little effort (T50 staples only join to very solid base materials, such as wood). Martin's victims, hysterical as they were, could have freed themselves from the T50 staples almost immediately.
Continuity mistake: At the end of the movie, the bloody handprint on the car changes entirely the second time it is shown. (02:02:45)
Other mistake: The initial view of Barrett's hospital room shows the lower portion of an IV pole. Barely visible IV tubes are hanging down, alongside (or touching) the pole. After briefly shifting to Sonny, there is suddenly a full IV drip bag. The IV tubes are no longer flush with the IV pole - they stick out on both sides and loop at the bottom. Also, the IV drip is not connected to Barrett. (00:50:29)