In short: It wasn't intended to be scary, but it turns out to be anyway.
The usual suspects of Accidental Nightmare Fuel include:
- Puppet, animatronic, claymation, or CG characters who were meant to be cute, but who instead look like they crawled out from the darkest depths of the Unintentional Uncanny Valley.
- Surreal animation, which can bring about a variety of unintentional horrors.
- Over-the-top slapstick violence, such as a character getting run over by a steamroller and turning into a flat photograph. It may seem funny to you, but imagine looking at such an event through the eyes of a literal-minded 6-year old.
- Sudden change(s) in medium between live-action, traditional animation, CGI, and/or Claymation, especially if it comes without warning and changes back just as quickly.
- Let's Meet the Meat, aka, disturbingly displayed talking food.
- Clowns, and not just evil ones.
- Mascot suits, and once again, not just the evil ones.
- Unnerving children's toys.
There is an excellent discussion about this phenomenon and its possible psychological origins in this blog post at The Onion A. V. Club. And check out the website Kinder Trauma — if you dare.
Contrast with Nightmare Retardant, Narm, and Faux Horrific. If the offending material can make you sick, you've got Nausea Fuel. For deliberately scary (but not very scary) kids media, see Defanged Horrors. Vile Villain, Saccharine Show is when a villain causes this in a show far more light-hearted than one would expect that sort of character to appear in. If it becomes scary only in hindsight, it's Fridge Horror.
Related: Unintentional Uncanny Valley