"High-Tech House of Horrors": S.H.A.R.I does a variety of terrifying things to the people trapped inside, but relatively few of them are lethal. She even does something off-screen to "rescue" the teenager she trapped in the flooding bathroom. Why? S.H.A.R.I's motive was to get attention; you can't get attention from a corpse.
The Great Dane impersonating Scooby in "Homeward Hound" is caught thanks to being unusually aggressive, going so far as to attack Fred when he accidentally steps on the dog's tail. The conclusion reveals that it was actually a small dog in a suit - which makes perfect sense when you consider that small breeds often have more aggressive temperaments, as was shown earlier in the episode.
In Fright House of a Lighthouse, the Creepy Keeper is attracted to Scooby in his mermaid disguise, which doesn't seem to make sense when the ghost turns out to be the female Verona Dempsey. However, there's two ways this can be taken that cause it to make sense: 1) It's a joke - Verona is an Expy of Velma, and it's long been rumored that Velma is a lesbian or 2) Verona did it to reinforce the facade of the monster. This gag would prompt the gang to think the villain is male if he fell for Scooby's disguise.
"It's Mean, It's Green, It's the Mystery Machine":
Susan Dinwittie could have easily committed vehicular homicide (she drove the Mystery Machine against traffic down a busy highway!) over something as trivial as a fad dying. There is no indication that she went to jail, meaning she could easily do it again.
When you realize two prepubescent children are in what appears to be the mainstream pop/rock scene. If you know anything about the music industry you will understand why it is a bad idea for prepubescent kids to be in the music industry at that age.
Also related to the Dinwitties, why do all the kids have rhyming names? It could just be Family Theme Naming, but, given what an obsessive Stage Mom Susan is, it's possible she was planning on making her kids music stars since before they were born and named them as a set accordingly.
What were Mike and the Bus Driver planning to do with Daphne? When Shaggy and Scooby found her she seemed very worried that the Leland Brothers would soon return. Also, when we first see her Bound and Gagged inside the mausoleum she looks distraught for a split second before being startled by Shaggy's voice, likely because she thought the light shining through the doorframe was the Brothers returning. Considering that they're already in a graveyard one possibility comes to mind.
Adding onto that, if the mysterious wail hadn't inspired Shaggy to use Daphne's phone to track her down, would she have been found in time?
"High-Tech House of Horrors": S.H.A.R.I's determination to get the attention she felt she deserved led her to trap multiple people inside the house, where she controls everything, including the climate and the food. Though she didn't seem interested in actually killing them (perhaps because that would decrease her "audience"), she would most probably have kept the group captive, experiencing situations like something out of a horror film to make sure they don't neglect to pay attention, if Velma hadn't outsmarted her.
