When Esme hits the guest on the ladder, she is wearing shoes, which are visible. In the next shot, she has bare feet.
When Esme's suit is fully inflated, you can see that the front part of the pants are still there. In the next shot directly after that, when Babe and Ferdy come running, you can clearly see that the front part is not there, even though she is in the exact same position.
In the first shot of Esme searching the crowded beach promenade for Babe, the building with the red "Eternity" billboard on top is clearly visible. However, earlier and later in the movie, the exact same building is seen directly behind the convenience store at the end of the same canal that the hotel is on and facing the hotel, indicating that sets were struck and rebuilt.
When Esme Hoggett arrives back at the Flealands Hotel after being released from prison. Her hair is extremely messy from the glue accident early in the film, But when she puts on the Clown Suit. Her hair is fixed up neatly into an updo.
The dog listed as the Pit Bull is actually a Bull Terrier. Pit Bulls look quite different, without the distinctive sloping muzzle of the Bull Terrier.
The orang-utan playing the part of Thelonius is a female, though the character is male. Male orang-utans have large, obvious cheek-pads, which are not present on this individual.
Pre-flight safety demonstrations are performed during taxi, not takeoff.
Babe recognizes Esme's voice in Fugly's apartment, but doesn't seem to when she's chasing after him in the hospital kitchen (he doesn't even know she's there until she enters the ballroom).
When Esme's clown suit is inflating and tearing her pants, you can clearly see she has rubber feet, an effect of having to put the inflatable suit on. Before, she had her normal, bare feet.
For some unknown reason Arthur Hoggett's daughter, son-in-law, granddaughter, and grandson don't come to see him when he gets severely injured in the well.