When Stuart is in the sewer, he gets wet. When he climbs out of the drain, he is dry again.
In the scene when George throws his pajamas down the laundry chute with Stuart tangled up in them the bottoms are already in the basket.
When the piano is being played, the note that gets stuck changes pitch depending on who plays it.
At the time when Uncle Crenshaw asks for his favorite "Little" nephew at the family gathering, Grandpa Spencer is not in the group shot. After switching shots and going back to the group shot, Grandpa Spencer is there.
At the end of the movie, the entire family goes back inside from the deck. Mr. and Mrs. Little, George and Stuart on Mrs. Little's outstretched hand. However, her hand is empty, Stuart is not there.
No front load washing machine would fill in the manner depicted. First, the water level would never be as high as it is shown, especially with such a small load. The washer would be partially full. Second, the water spigot would not be in the rear of the machine, let alone mounted on the drum. It would be either above the door or in the area around the drum, but not mounted on it. Third, once started, the machine would most likely tumble while filling, or at least do some tumbling before "deciding" on a load size (and thus, "deciding" on how much to fill, how much time it will take, etc.). This machine appears to behave more like a top loader, in that it fills completely and then washes.
The Little family's washing machine's "Door Locked" light turns on when Mrs. Little starts the washing machine. However, she opens the door of the washing machine to free Stuart out of there without pausing it first.
Stuart Little loses his roadster while he falls into the storm drain and it is never seen again for the remainder of the movie. In the sequel however, he seems to have recovered it without an explanation.
Mrs. Little starts the washing machine without adding detergent. It's possible that there was already detergent in the machine (since it's a front loader), but when we see Stuart in the machine for the next few minutes, the water is clear enough to be rinse water (without detergent).
When Snowbell is trying to convince Smokey not to attack Stuart, he says that Stuart has his own car. However, earlier in the film, Stuart drove the car off the edge of a pipe into the water below, resulting in the car sinking.
Mrs. Keeper's job is to help the orphans get adopted. They want to adopt Stuart but she says, "Mr. and Mrs. Little, we try to discourage couples from adopting outside of their own... species. It rarely works out." If she discourages couples from adopting the orphans, then what is the adoption agency for anyway? Different species adopt different species all the time and it works out most of the time.