When Stuart is adopted, George gives him the cold shoulder, refusing to believe that a little mouse could ever be a true brother to him. When the entire family comes over to meet Stuart and encourage him and George to play together, George torpedoes the entire event when he again disavows Stuart, saying "He's not my brother! He's a mouse."
When the Stouts come to take Stuart away, after both he and the Littles have bonded with each other.
The simple fact that Stuart's parents died grocery shopping when a massive stack of cans collapsed on them. It also alerts the Littles to the fact that the Stouts were not who they said they were, and they realize Stuart's been kidnapped.
When Stuart arrives at the Little house—just seconds after the family leaves to search for him— only for Snowbell to lie that they were happy he was gone pointing to Stuart's empty face on the family photo (which they actually used for his lost posters) and Stuart leaves, heartbroken. As soon as he's gone, Snowbell immediately regrets his actions.
For Stuart Little 2:
Just as Margalo is enjoying her stay at the Littles, Falcon threatens her to steal Mrs. Little's ring or he'll kill Stuart. Margalo already felt guilty for stealing the ring (and the family think it's fallen down the kitchen drain), but after she saved Stuart from going down the drain, his gratitude to her makes her only feel worse.
Stuart: Margalo, you're the best friend I've ever had. (hugs Margalo, who sadly hangs her head in guilt)
Later that night, Margalo gives a sleeping Stuart her precious jeweled stick-pin, before leaving the house out of guilt and shame.
Margalo: I'm sorry, Stuart. (sadly flies out the window)
The moment where Falcon drops Stuart off the building and Margolo thinks he died, triggering a My God, What Have I Done? moment.
Later when Snowbell comes to rescue Margalo, and she tells him Falcon killed Stuart, and Snowbell breaks down in tears. Of course, neither of them knows he survived.
