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.
Cross-Dressing Voices: Pajama Sam has been voiced by three women: Pamela Segall Adlon, E.G. Daily, and Elisha Ferguson.
Rudy Beagle (AKA Mr. Forklift) did not have a space for Sam to ride in in Thunder And Lightning Aren't So Frightening. This was changed in Lost & Found.
Non-character example: Sam's copy of Pajama Man issue #1 has a different cover in Life Is Rough When You Lose Your Stuff! than it did in No Need To Hide When It's Dark Outside.
Development Gag: The observatory puzzle, wherin Sam has to wear a pumpkin on his head to get past a pair of guards, is a nod to Sam's original character design. Yes, according to Ron Gilbert, he was originally designed as Pumpkin Head Boy.
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