In "All In", it is made clear numerous times that House has memorized Ester's file. However, when he spells it on the white board, he spells it Esther. The sticker on the file he pulls out clearly reads Ester, as do the subtitles on the DVD from the Season Two box set. Wouldn't someone who has taken as extreme an interest in this case as House be able to spell her name right? A possible explanation pointed out to me was that the file could have been a copy of the unofficial file as House wouldn't have been allowed to keep the official file. It was assumed that the file label had a typo. This does explain a lot and I therefore fully embrace this theory, and scold the people with the label maker.
Also, his parking space changes between the episodes. In "Mob Rules", when he is looking for his car (and discovers the Mustang), he is in a parking garage. Then, in "Daddy's Boy", there are at least two (off of the top of my head) shots of House's bike being outside in a parking space. Later, in other episodes such as "Lines in the Sand", and "Cane and Able" his bike is parked in a parking garage again. I am no expert on how hospitals are run, but are people really allowed two parking spaces- one outside and one inside. I kind of doubt that, but then again I take pride in only being in the hospital as a patient at birth!
Another (more obvious mistake) is that his birthday was clearly around December in "The Socratic Method", but in "No Reason", his birthday (on the I.D. tag on his wrist) said his birthday was in June, which David Shore verifies in the commentary by stating that it was Hugh's birthday used there. It could be excused because it was in fact a hallucination, but wouldn't someone as observant as House notice they had his birthday wrong?
None of these are major but still, they are large enough where someone as obsessive as me gets annoyed. Any Comments, Questions, or Concerns are welcome and appreciated.