Cowboy Bebopat His Computer: In the Captain America episode of Loose Canon, Lindsay says Marvel 1602 is set on the Roanoke Colony in Virginia! While the city of Roanoke is indeed in Virginia, the "lost colony" and therefore the setting of the book is in what is now North Carolina.
In the Death episode of Loose Canon, she misgenders Grell, referring to her with male pronouns.
Development Hell: There was talk of making a home site (like Angry Joe's, a place for stuff that they couldn't put on TGWTG), resulting in Chez Apocalypse. It was functional for several months and hosted other shows as well, but after Blip and Maker shuttered their doors, development of the site returned to square one.
Fandom Nod: After fans shipped Mara Wilson with Critic after just her enjoying his humiliation in A Simple Wish, Matilda ups the Foe Yay aspect with her acting like he was a really fun toy to play with.
Missing Episode: After deciding to leave Channel Awesome, Lindsay intended a review of the Animorphs TV series to be her last one using the Nostalgia Chick character. She did film the episode, but was not satisfied with it and decided not to release it, making her first Loose Canon episode ("Starscream") also the last official NC video.
Old Shame: In her livestream, Lindsay admitted that she watched "Rapping About Rape" again and could see why it got so much hate.
In a weird way, the TLC retrospective. While she doesn't seem to think it's a bad episode, it's more that she thinks sincere emotions on the show are too out of place.
Her review of the Dune film. Lindsay took it down because she felt that most of the plot holes she brought up were actually addressed within the film itself, as unclear as they were.
Her crossover review with the Nostalgia Critic for Moulin Rouge!. She legitimately enjoys the film, but since Doug Walker wrote the script for the review, he mapped his own opinions onto her lines. Lindsay talked about her regret for agreeing to do the review on her Twitter.
The one part of the review she did write was the "anti-Christian diatribe," which she also rescinds.
In her commentary for X-Men, Lindsay said she was going to follow the TGWTG trend of having more than one character and play Dr. Tease herself.
The same went for Dr. Block, but because Lindsay hates acting so much, Nella took the role herself.
The Nostalgia Critic was going to review Newsies, but Lindsay told Doug she expressed interest in reviewing it, so he let her do it instead.
In the Les MisÚrables big group song, Ed Glazer or Doug could have played Marius instead of Paw, it could have been a chorus of Lindsays (recorded to set everyone's place, as described in the commentary), or the review might not have happened at all due to Lindsay and Elisa having a car accident on the way to Chicago. (A hurricane just made them swerve into a ditch, they were fine.)
In an example that made shippers' hearts soar, the first "Thanks For The Feedback" was going to see the Chick and Critic have sex, and then realize they were related.
As charmingly goofy as it was, the Dark Nella Saga was going to be much sillier and originally consisted of the eponymous quasi-demonic force of evil giving everyone evil noogies.