The Cast Showoff: Daphne gets to sing, not one, but two songs in the episode "In Fear Of The Phantom". Grey DeLisle knocks both right out of the park.
Creator Backlash: Derrick J. Wyatt doesnt like when the franchise involves real monsters and supernatural threats and tried to campaign for the removal of the central supernatural Myth Arc, but was overruled.
While nothing specific was stated, Mitch Watson said that some ideas were shot down for being too scary or weird by the "powers that be".
Velma's relationship with Hot Dog Water couldn't be explicitly stated as a romantic one due to resistance from higher-ups, leading to their status later being confirmed by Word of Gay.
Fandom Nod: In "Dance Of The Undead", when asked why the Hex Girls went back to their original outfits (resembling the ones worn in Witch's Ghost), they say that fans just preferred their original look. Some fans complained about their new look, so this is more than likely a little in-joke.
Fan Nickname: The Nibiru Entity is actually referred to as the Evil Entity in the series proper.
God Never Said That: Although Mystery Incorporated Velma is confirmed by Word of Gay to be lesbian, this has been taken by the general audience to mean that all her incarnations are lesbian, likely due to people not being aware that Scooby-Doo has multiple continuities. This is despite her showing interest in men without issue, including Shaggy, in various films.
Judy Reeves is Fred's mother, as the flashbacks in Season 1 depicted her as having a Strong Family Resemblance to Fred. Also to a lesser extent, Brad Chiles is Fred's real father. The Season 1 finale would confirm this.
Cassidy Williams and Angel Dynamite having some sort of relation, possibly because they're the same person. This was confirmed near the end of Season 1.
Mayor Jones being divorced from Fred's mother (or more accurately, she left him). Confirmed in "A Haunting In Crystal Cove", or at least that's what his cover story was.
Mayor Jones is involved in the show's Myth Arc via the disappearance of the original Mystery Incorporated, and is not a trustworthy figure.
Betrayal broke apart the original Mystery Incorporated because of Pericles.
Jossed: Many people liked to believe that Cassidy survived the underwater explosion, and that she was just hiding. This was not the case, as she does not reappear until the timeline had been reset.
Non-Singing Voice: Averted with the Hex Girls and Daphne. All of the actresses performed the songs played within the show.
Referenced by...: Young Justice episode "First Impression" has the Newsgirl Legion teens Tommi Thompkins channeling Fred, Gabi Gabrielli channeling Daphne, and Big Words channeling Velma (who even has a brief gag about losing "[her] spectacles") as they conduct a mystery investigation in their small town of Brooklyn. Tommi shares her name with her father, Mayor Tommy Thompkins, who not only doesn't bear any physical resemblance to her at all, doesn't want her and her friends conducting investigations, to the point that he's willing to have them arrested. Mayor Thompkins and Sheriff Patrick Maguire also resemble Mayor Jones and Sheriff Stone in terms of physical appearance and mannerisms. Additionally, Sheriff Maguire's voice actor, Troy Baker, does an impersonation of Patrick Warburton's performance. And per standard of Scooby-Doo media, the episode's villain, Whisper A'Daire, complains as she's arrested that she would've gotten away with it if it wasn't for Those Meddling Kids. Greg Weisman, one of the show's co-creators, is a friend of Victor Cook, one of Scooby-Doo! Mystery Incorporated's head writers, as they've both previously worked on The Spectacular Spider Man together. The show's other co-creator, Brandon Vietti, also worked on some of the Scooby-Doo DTV films, including Scooby-Doo! WrestleMania Mystery, which contained a cameo appearance from Megan, Zatanna, Artemis, and Cassie.
Role Reprise: Starting with this series, Matthew Lillard takes over as Shaggy's voice actor, reprising the role from the live action theatrical films.
Screwed by the Network: Despite universal praise the series was screwed in Season 2 where there would often be months between new episodes and no news of when new episodes would come out. It was easier to find the episodes online rather than TV. Luckily however, they managed to wrap up the series at the end instead of outright canceling it like many other shows that have been screwed.
Shrug of God: When asked if there were any LGBT characters on the show, Victor Cook stated that there were "none that [he was] aware of.", even when Hot Dog Water was suggested.
According to early press releases, the story would have been somewhat different, as the gang is only visiting Crystal Cove instead of having grown up there:
The kids from Mystery, Inc. arrive in the village of Crystal Cove, a small town known for its many ghosts and ghoulies. Fred and Velma are determined to debunk the area's many paranormal phenomena.
But it turns out the locals are none too eager to have their mysteries quashed! Will the gang's head for logic prevail over centuries of local legend?
The Freak was originally named "The Fiend".
Pericles was considered wearing a mask based off of Hannibal's.
Judging by the credits of "Mystery Solvers Club State Finals", the Black Knight from the very first episode of Scooby-Doo, Where Are You! was supposed to appear, possibly voiced by Gary Cole. He is also credited with reprising his role as Mayor Jones, who doesn't appear in this episode either besides a name drop.