When Sarah shows Michael the scars on her back she is obviously not wearing a bra. Moments later when they are shot at and run outside, she is wearing one.
In the scene where Micheal has a bloody nose we see blood on the side of his hand, it is gone when the camera switches angles.
After accepting Self's offer to track down Scylla and reuniting with Sara, Michael decides to have his tattoos layered off. Later, when Michael is shown with his shirt collar open at the neck, there is no indication that there were tattoos there or that he has any scarring due to lasering the ink off. Michael's tattoo went clear up to his neck so the skin shown bare is incorrect.
When Mahone recognised one of the card holders driver, he asked for a list of Males aged between 45 - 55 ....
When the results came back and he picked him out as the driver, it stated that the males date of birth was 1980, at the time he would have been 29, so would not have been picked up in the age range he asked for.
Michael's tattoo is removed in a single, albeit lengthy session of laser treatment. In reality, removal of even small tattoos is an extended process of several sessions.
The slip of paper with "Scylla" written on it had the impression of the word on it as if someone had written the same, single word before on the notepad, torn the sheet off and written it again.
Between time mark 21:31 - 21:33, the face of the stunt double for character Lincoln Burrows is clearly visible during the fight scene.
When T-bag reads the paper about his so-called 'friend' (James Whistler) being murdered, the paper article does not match the report about the 'local salesman found murdered in alley'.
When looking for card holder's driver, Mahone suggests searching for males aged 45 to 55. The printout of driver's record shows the picture of approximately 50 years old male. However, the birthday on the record is 1980, which makes the driver approximately 28 years old.
While Agent Self is talking to his contact Jasper at a car lot a car for sale is marked as being a 2007 model even though the time line of the story would still be set in 2005.
When Michael types in the Internet address, we see http:\\www.EuropeanGoldfinch.net\ which is of course incorrect. The backslashes should have been forward slashes (although most browsers will still bring you to the correct site).