* CaptainObviousReveal: [[spoiler:Velma's]] conspicuous absence from the opening scene combined with the gang's shocked/confused reactions when they unmask the witch can make the TheReveal a tad bit predictable, especially if you catch yourself wondering: "Wait a minute, [[spoiler:why isn't Velma there?]]". It doesn't take a observant viewer to notice she's been absent almost every time the Frog Monster appears besides the RedHerring, and her behavior is a little uncharacteristic, like thinly-veiled excuses in her trying to sabotage the investigation.
* HoYay: Scooby's jealousy of Shaggy's relationship with Velma is viewed less like a jealous pet and more like a jealous friend who secretly likes Shaggy. Heck, the last scene just before the end credits has hearts show up while Scooby and Shaggy hug.
* ItsTheSameNowItSucks: Some fans criticized the twist of [[spoiler: Velma being the culprit]], since it was already a twist in ''WesternAnimation/ScoobyDooInWheresMyMummy''
* {{Narm}}: [[spoiler: An ''ancient evil witch spirit'' giving the YouMeddlingKids line as she's being dramatically exorcised kind of brings you out of an otherwise tense moment.]]
* RomanticPlotTumor: While Fred/Daphne and Shaggy/Velma are relatively well-liked pairings, this movie makes them less charming to the fanbase.
* {{Sequelitis}}: ''[[Film/ScoobyDooTheMysteryBegins The Mystery Begins]]'' is already a divisive movie but this installment is universally regarded as inferior, by an excessive focus on the romantic subplots and a rather obvious and uninteresting mystery.
* TheyWastedAPerfectlyGoodCharacter: Scooby's noticeably OutOfFocus here, with the more focus on the RomanticPlotTumor.