In the last episode when Zimbulu opens the chest, three random ghosts come out (not seen earlier in the series, which is most likely a cost-cutting measure). Earlier in the episode, in a throwaway line, Vincent mentions they are trailing a ghost that keeps eluding them, and we see in the episode that Zimbulu's chief plan is to send other ghosts/zombies after the gang, meaning they were probably his minions they captured prior to the episode.
Frankenscoob's monster in "That's Monstertainment!" acting extremely affectionate towards Scooby-Doo makes perfect sense when you realize that technically he's only a few minutes old (being brought to life a short time earlier in the same episode) and Scooby was the one to reanimate him (hence calling Scooby "Mommy").
It calls back to the original Frankenstein tale, where the monster only wanted companionship. Unlike Victor Frankenstein, who refused to accept his monster and sought to hunt him down, Scooby is a lot more openhearted and accepting.
Even if this show was in the same continuity of Mystery Incorporated, (where Flim-Flam was said to be serving a 25 to life prison sentence), his return in this series still makes sense in a few ways. First, he could have reformed and got time off or paroled for good behavior. Second, (and more likely), the original series established that he's a wily Con Artist with a HammerspaceBag of Holding in his hoodie. Does anybody really think that prison would be able to hold him for long?
The decision to use the score of The Great Grape Ape as the music for Platypus Duck seems like a straight forward case of recycled bits. While this was probably unintentional on the writer's side this seems to have been a clever joke from the musical director side. Grape Ape started life in a package show that included The Tom and Jerry Show and later Mumbly. When these shows were split up in syndication Tom and Jerry and Mumbly got the old show's theme recycled with altered lyrics. Grape Ape got a whole new song. Of all the characters themes to use here, there's hilarious irony it was the one who actually avoided using one in the first place.
Scrappy's minor arc in Scoobra Kadoobra. When Daphne gets put into an enchanted sleep, he immediately can tell that something's wrong, as he is in tears about it and sadly asks her to wake up, but is quickly seen focusing on the battle with Maldor later. It was simply just too sad to keep trying slim shots at breaking Maldor's spell and getting a No-Sell. We see how emotionally wrecked Shaggy, who was in denial longer, became. Focusing on something else was a coping method.
