The Incredibles was the biggest offender in my childhood: it was sensory overload for me from the workplace scene to the jokes to the villain all done in a viciously brutal Pixar story formula.
Despicable Me was another contender because that film I don’t consider friendly to kids now, because characters are jerks and the villains are the minor ones pulling all the strings (Miss Hattie and Mr. Perkins scared me badly).
Tangled, mostly because of Mother Goethe verbally abusing Rapunzel and stabbing her boyfriend in the stomach only to get killed.
Wreck-It Ralph also has everyone hating on Ralph for being a villain, Vanellope gets shoved into a puddle of chocolate by her own kind, Calhoun is an abusive bastard, Turbo doesn’t even belong in a movie meant for kids as a villain even though he dies a goofball later.
Transformers: Age of Extinction, mostly because of Joshua Joyce abusing his role although the rest of the movie was okay.
Marvel’s Avengers was fine, but Bruce Banner/Hulk and Loki were convincingly scary.
HONORABLE MENTIONS:
The Boy and The Beast was a brutal coming-of-age film, but I saw it when I was a teenager.