- Cargo Ship: Once again, Fred and the Mystery Machine. He even refers to it as "my love".
- Fridge Brilliance: Another reason the gang failed to recognize the Sheriff as past enemy Cutler Toe — aside from lack of a beard, hat covering the baldness, and altering voice and demeanor — the picture of the unmasking from his monster disguise shows that the gang found Toe's oufit so disgusting that none of them could stand to even look at him directly.
- Inferred Holocaust: The town of Crystal Cove (or at least the town square judging by later dialogue) is presumably destroyed by collapsing into a cataclysm, possibly killing god knows how many people assuming they didn't evacuate in time.
- Just Here for Godzilla: Even if you don't regularly watch the Scooby-Doo movies, you may decide to give this movie a go if you're a Batman fan to see the appearance of The Scarecrow. Or if you're a fan of Bill Nye and/or Elvira, either of them could be strong selling points for the movie as well.
- Les Yay: Daphne is really into Elvira.
- They Wasted a Perfectly Good Character: Even ignoring those who don't have that much of a problem with Scarecrow being the main villain for a second, many fans were still disappointed to find out that despite being heavily advertised as such that his total screen time only amounts to five minutes, with his only major moments being at the beginning and then towards the end of the second act, feeling like a bit of a waste especially since Dwight Schultz is clearly giving it his all as well as the interesting Worthy Opponent dynamic he has with Velma. The most common speculation being (like most behind-the-scenes aspects of the film) Executive Meddling, specifically from the DC Comics side of things.
- Unexpected Character:
- Jonathan Crane aka The Scarecrow is featured in what at first is an antagonist role but turns into a support role.
- Elvira is also pretty surprising due to not being traditionally associated with family entertainment (well, outside of Knotts' Berry Farm anyway) and being pretty obscure to most people born after The '80s. However, this marked her second inclusion in this Scooby series.
- To a lesser extent, Bill Nye also put in an appearance on Scooby-Doo and Guess Who?, but him also appearing in a Direct to Video movie was surprising.
- The return of the Sheriff is a near aversion, only because after he returned in the previous movie some were expecting he wasn't done.
- Due to Red Herring not having appeared in any Scooby Doo media since A Pup Named Scooby-Doo, seeing him briefly return in a cameo appearance with his own Halloween-themed business can come as a surprise.
YMMV / Happy Halloween, Scooby-Doo!