In the One-Stop Fun Shopstorytime coloring book storyThe Lost Socks, if you choose to have one of the trees from the first game in the story, they refer to it as Mrs. Tree. Not only did they misidentify her as one of the custom inspection trees, but her name is Ms. Tree.
In the Tie-In NovelPajama Sam: What's Different?, the banner at the sweets' party reads "Welcome S.A.M." instead of "Welcome S.S.A.M." despite optional dialogue in the game pointing out that it's supposed to be spelled with two Ss.
A different Chess Bleachers areanote mentioned in one of the Debug Rooms
A Contact path (an alternative to the Putty path), in which Grandma Sweater would not have needed a pattern, instead losing one of her contact lenses and needing the lens foundnote mentioned in Dummied Out dialogue
Dr. Grime being named Dr. Filthnote mentioned in one of the Debug Rooms
The fire truck ladder rotatingnote mentioned in Dummied Out dialogue
A Lampcord area (from which the Sidetable Top, had it existed, would have been accessible) located between the Vista and the Elastic Wastelandnote mentioned in one of the Debug Rooms and in Dummied Out data
The peanut sometimes being found at the Dust Bunny Corral instead of at the Vistanote mentioned in one of the Debug Rooms
A Sidetable Top area (which would have been accessible from the Lampcord, had it existed) with some sort of connection through the Elastic Wasteland to the Dresser Scaling mini-gamenote mentioned in one of the Debug Rooms and in Dummied Out data