Fanon Discontinuity: Almost completely disowned by fans of the classic cartoons who detest this film for abandoning everything central to the comedic duo.
Follow the Leader: The pathos filled orphan plot? The musical numbers? The hammy bad guys (one of whom is voiced by Tony Jay)? Its very obvious that the film was a shameless attempt at cashing in on Disney's renaissance during the early 90's, with Tom and Jerry thrown in for marquee value. Suffice to say, it didn't work.
Misblamed: Though the film makes it seem that Tom and Jerry have never talked before the events of the film, in reality many of the early shorts feature Tom and/or Jerry speaking, with Tom speaking much more frequently than Jerry.
Nightmare Fuel: The aforementioned "Dr. Applecheeks closing in on the ice cream cart" moment. Brrr. His character in general counts, actually; portrays himself as a kindly vet who loves animals and allows people to drop off lost pets for him to take care of. But then he shows his true colors, as a greedy con man who makes money off of pets that he kidnaps and sells back to their distraught owners. All the while, he abuses the poor little creatures and treats them less like living things and more like money-making commodities. Even his own henchmen are terrified of him.
Older Than They Think: This isn't the first time that Tom and Jerry are changed from mortal enemies to best friends. The Tom And Jerry Show had the duo as friends and aired 17 years before the movie hit theaters. Problem there though is that's when the shorts were undergoing Seasonal Rot and aren't highly regarded by fans either.
Tom and Jerry also talked and sang occasionally in the original shorts.
Paranoia Fuel: Barring Robyn's father, literally every adult character in the movie, even the ones who seem nice at first, turns out to be a villain.
The Scrappy: All of the new characters created for this movie; Pugsy, Frankie, Aunt Figg, Lickboot, Captain Kiddie, Squawk, Dr. Applecheeks... and especially Robyn Starling, the girl that Tom and Jerry help to find her lost father, and the one responsible for making Tom and Jerry stay Out of Focus and making the movie being about Tom & Jerry In-Name-Only. The few that aren't universally reviled (Lickboot, Applecheeks to name a few) are only liked because of YouTube Poopremixes and memes.
Pugsy deserves a special mention, as he is the one who got Tom and Jerry to talk and sing about how they are best friends, despite Tom and Jerry being, you know, mortal enemies.