These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
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.
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.
Squick: Aunt Figg and Mr. Lickboot look like they're about to kiss at the end of their Villain Song.
They Changed It, Now It Sucks: The general reaction of existing T&J fans to the movie making such drastic changes in tone and content from the original shorts.