Biology 101 - S3-E1
Visible crew/equipment: At the beginning of the episode, after Pierce rejoins the group and Jeff and the others begin to leave the room, watch Britta as she stands up. When she turns away from the camera, you can see the actress' microphone-pack in the back of her jeans briefly. (It's hard to spot but it's there, and is confirmed in the commentary track.).
Geography of Global Conflict - S3-E2
Continuity mistake: When Annie starts to throw her tantrum, she knocks stuff off the table, including the microphone and small mic stand. When she's lying on the table, the mic stand is back on the table. It back on the floor when she and Jeff leave, although the Uruguay sign is now back on the table.
Geography of Global Conflict - S3-E2
Continuity mistake: When Britta is in a cage, before Chang walks in, a couple pass her and are walking out the double doors, where both doors are open. After Chang steps up to the cage and the camera shot changes, the couple is further away from the doors and walking out again, only this time one of the doors is closed.
Other mistake: Since Annie had completed the terrarium the group should have at least received a passing grade since the Professor made them a group of 7.
Advanced Gay - S3-E6
Continuity mistake: We know from this episode that Pierce's father is alive, but at the beginning of episode 1-7 Pierce's mother is on the other end of the phone and speaks about seeing his father's "ghost," as if his father has passed away. (00:02:00)
Suggested correction: Pierce explains in a later episode that his mother liked to believe that his father was dead.
That's not a proper connection. Her "liking to believe" his father was dead is not her literally thinking he's dead- she just wishes he was dead. So she should know enough to know she couldn't have been seeing his ghost. It's a mistake because they decided to write Pierce's father into the show on a later date.
Foosball and Nocturnal Vigilantism - S3-E9
Character mistake: In the bonus clip where we see Leonard's online video about frozen food, the first thing he says is, "This is November 29th". However, if you look under the video, you can see the video was uploaded on Nov 26, 2011, which is three days earlier.
Digital Exploration of Interior Design - S3-E13
Continuity mistake: Britta sets down her copy of 1984 and her pen, which is angled with the end pointing away from the book. Two cuts later, the pen is now parallel with the book, without Britta ever touching it.
Audio problem: Jeff summons Abed and Troy to meet together, saying "this has to stop," to which Abed replies "tell him." But the audio was cut abruptly at the start of his sentence and we can only hear "ell him."
Origins of Vampire Mythology - S3-E15
Continuity mistake: The way Britta holds the banana from the DVD cabinet changes between shots.
Virtual Systems Analysis - S3-E16
Continuity mistake: When Annie is talking to Abed in the study room, next to Troy and Britta, the Dean's "Puttin' On The Ritz" cane is leaning against some books, towards the right. When the Dean comes back in to claim it, it is leaning towards the left.
Course Listing Unavailable - S3-E18
Continuity mistake: The stars Britta puts on change during various shots. She wouldn't have had time to readjust them when off camera either, and at the end when she tried to remove them, they're stuck on pretty good.
Course Listing Unavailable - S3-E18
Continuity mistake: As Jeff makes his way to the podium to say a few words about Star-Burns, Pierce is sitting next to him with his hands on a table. Light applause breaks out and in the next shot, Pierce's hands are raised up near his face as he's about to clap.
Course Listing Unavailable - S3-E18
Continuity mistake: When Jeff begins crying with his head down on his text book, Britta attempts to comfort him. She touches his hand and he swats it away, but in the next shot his hand is gripping the pages of his textbook.
The First Chang Dynasty - S3-E21
Continuity mistake: Troy and Britta are spying on the school behind a hedge through binoculars. When Annie pops up, Troy sets them down. As the camera cuts between Britta and Annie to Troy, the binoculars disappear and reappear.
Introduction to Finality - S3-E22
Other mistake: During Leonard's "Let's Potato Chips" YouTube video during the ending credits, you can see the video reaches the end of the load/play bar (watch the circle), yet the video continues for several seconds. Once the circle reaches the end of the load/play bar, the video is over and won't continue.
Introduction to Finality - S3-E22
Continuity mistake: After Alan tells Jeff that he turned him in to the state bar, he gets up and Jeff thanks him. Two quick shots later he is impossibly close to the door.