The Habitation Configuration - S6-E7
Continuity mistake: When Howard is almost done moving out of his mother's house, there is a table in front of him with a measuring device in the top corner. In one shot, the device moves to the opposite corner of the table. In a few shots later, the item returns to its original position.
The Spoiler Alert Segmentation - S6-E15
Revealing mistake: Throughout the series much is made of the fact that Howard's mother is grossly obese, and in The Engagement Reaction (S4 E23) it is even mentioned that her arms are hugely oversized. However, at the end of this episode we see her arms when she grabs Raj to stop him climbing out of the window, and they are the arms of an average-weight woman - they aren't overweight at all.
The Higgs Boson Observation - S6-E3
Continuity mistake: At the end, when Alex and Sheldon are at the apartment, when Alex says "she seems nice", there are two beer bottles on the coffee table. The camera goes to Sheldon, and when it returns to Alex, there is only one bottle.
Other mistake: When Howard, Stuart and Sheldon are ringing the bells, they are ringing differently from the "code" (00:16:45)
The Cooper/Kripke Inversion - S6-E14
Character mistake: As Leonard is leaving the Mechanical Engineering lab, the sign on the door is spelled incorrectly as 'resticted area' instead of 'restricted area'. (00:04:07)
The Habitation Configuration - S6-E7
Continuity mistake: When Wil first enters Fun with Flags, he has his flag partly on the table in front of him. In the next shot, the flag is not on the table at all.
The Spoiler Alert Segmentation - S6-E15
Other mistake: When Leonard and Sheldon are about to make up, you see green lights flash in the hallway. The next shot you see the hallway and it's completely normal.
The Parking Spot Escalation - S6-E9
Continuity mistake: In this episode Penny mentions she has a sister ("I remember my first bikini wax. My sister did it with duct tape and melted Crayolas"), but in future episodes she has only a brother.
Suggested correction: While her brother was the only one that came to the wedding she mentions her many other times and never said she only had a brother. She mentions her father dancing with her and her water breaking at her wedding. She asks her dad about Randall and Lisa. She also mentions her sister "accidentally" shot her husband. So while the brother is more prominent the sister is mentioned throughout.
The Parking Spot Escalation - S6-E9
Other mistake: Sheldon tries and fails to move Howard's car at the start of the episode. However if you look closely the car does roll backwards even though the handbrake is applied.
The Closure Alternative - S6-E21
Continuity mistake: Sheldon and Amy are talking while drinking tea together. The entire time, Sheldon has his hand next to his other hand, but in an individual shot, his hand is suddenly on his other wrist.
Suggested correction: There is a moment when he puts his hand there. So nothing wrong here.
The Higgs Boson Observation - S6-E3
Factual error: Sheldon tells Alex that he's run a background check, including her medical records. There is no way he could obtain medical records without a HIPAA authorization signed by Alex herself. It's illegal.
The Higgs Boson Observation - S6-E3
Other mistake: Just before Amy video chats Sheldon there is a shot where she is wearing glasses, and when the camera zooms out she isn't.
The Extract Obliteration - S6-E6
Continuity mistake: Sheldon is sitting by himself at a lunch table with an opened bottle of water with the bottle cap in front of the bottle. Raj and Howard arrive, and in one of the shots, the bottle cap moves closer to the bottle by itself.
The Higgs Boson Observation - S6-E3
Continuity mistake: Sheldon is taking composition books out of a box that was sent to him. When he first starts pulling them out, he has two composition book in one hand. Two shots later, he has only one composition book in his hand, but he is picking up a second one.
The Extract Obliteration - S6-E6
Continuity mistake: Sheldon is siting at the kitchen counter with a mug in front of him. In one shot, the string of a teabag appears coming out of the mug. In between shots, the teabag string moves by itself.
