A New Day in the Old Town - S2-E1
Other mistake: The killer from another dimension shape shifts into the appearance of the victim, leaving the victim's body. But it transforms into Charlie's appearance and leaves behind its former female nurse shape, hiding Charlie's body to dispose of later. It would have needed to transform from the nurse shape, not out of nothing. The original nurse's body was not at that location.
Suggested correction: The shapeshifter transformed into Charlie using his dead body which it then disposes of at the end of the episode.
But when the shapeshifter transforms into Charlie, he shouldn't be leaving the body of the nurse behind since he had killed the nurse before entering the hospital and transformed there into her. The only dead body in that last scene should be Charlie's.
Other mistake: Carrie the assistant brings Lisbon and Jane to Stutzer's office. She swipes her card to open the door. However, she does this upside down, swiping the bar-code instead of the black magnetic strip, on which she is holding. (00:09:30)
Home for the Holidays - S11-E1
Other mistake: Only one set of prints were said to be on the garrote but in the last episode of season 10 Graham handles the garrote before handing it over to the murderer without wearing gloves. So there should have been 2 sets of prints.