Ass Pull: In "Night of the Living Burger" the gang are able to simply order a Bucket O' Clues. What makes this worse is the guy who served them was the culprit. Although, the clues he gave were misleading.!
They Changed It, Now It Sucks: Others, particularly older fans of the original cartoon, loathe it for its ham-fisted attempts at parody, the overuse of cliché cartoon sight gags, and the entire Spin-Off Babies angle of the show.
Ear Worm: Not only does the main theme try to be as infectious to your ears as possible, but even most of the other music when characters aren't talking draws from it or its repetitive character title singing, meaning you're gonna hearing a whole lotta Scooby-Dooby-Doo.
Fridge Horror: As a certain fanfic pointed out, Red Herring probably would come to resent Fred both for all those times he falsely accused him of various crimes, which probably didn't help his adult reputation, and for eventually becoming a fairly respected detective. And the scenario presented, someone angry at the gang going after Velma, is disturbingly plausible...
"Funny Aneurysm" Moment: In "Scooby Dude" the gang busted a drug dealer. Freddie's voice actor, Carl Stevens, would later become a drug addict and was found dead from a heroin overdose.
Vindicated by History: This show was lambasted back in its day for its repetitive animation (especially seen in its dance montages), formulaic nature and for contributing to the trend of "babyfication"note making kid versions of popular '60s/'70s and earlier shows that was going on for cartoon franchises in the 1980s. Nowadays it's fondly remembered for being the first Scooby-Doo series to not take itself seriously by frequently lampshading and parodying the clichés and tropes of the original formula, paving the way for later incarnations.