Tracking down and handling dog skulls is a major part of the plot. It is also assumed that Dastardly's dog died, though he is later revealed to be alive.
No children are abused, though it's worth mentioning that Dastardly's robot minions are made to look similar to babies, and Dastardly yells at one of them and rips off its head to throw into a furnace.
After Dastardly finds his dog, he knocks the dog hard on top of his head. During the final fight scene, a giant dog monster is beat up and hit with an explosive.
Dastardly yells at one of his robot minions, then pulls off its head to throw into a furnace. Additionally, there is a robot dog with a head that looks like a real dog head put onto a robot, but it's clear that it's a robotic head as the movie progresses.
The head of the one of the antagonist's robots (portrayed similar to minions with personalities and emotions) is ripped off, thrown into a furnace, and is replaced with a vacuum.
Cerberus appears to be a ghost of some sort. In true Scooby Doo fashion, the ghosts shown at the beginning of the film are all revealed to be humans dressed as ghosts. However, in the first encounter with a "ghost", its portrayal is convincing at first.
Moments after the characters first encounter a stranger on the island under the mountain, the stranger warns them about dinosaur poop, and a big pile is shown seconds later.
There are no Jewish characters or comments about Jewish people, though it's worth mentioning that during a discussion with a police officer at the side of the highway the group discusses how 'ugly' the villian's (who is obsessed with finding treasure) large hooked nose is.
A man disguises himself as a woman police officer for a minute, though there is no pronoun use or direct reference to gender in relation to that scene, so there is technically no actual misgendering.
No planes crash. However, after the Blue Falcon's plane is destroyed off screen on the ground, the van has plane wings and engines strapped onto it, and it crashes.