These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Crossover Ship: Despite the fact Frank's still with Callie, he and Nancy Drew are pretty cozy pals...
Ensemble Darkhorse: Vanessa Bender, Joe's second girlfriend in the Casefiles who despite not having appeared in the books since that series' cancellation over ten years ago still makes regular appearences in fanfic.
Chet Morton. Dear God, Chet. He has appeared in the most books out of any non-Hardy, and was so popular that in 1965, they were considering giving him his own book series, which never got past the planning stage.
In a more meta sense, the Casefiles themselves are an example of this. Removing the typical roadblocks of No Hugging, No Kissing, Never Say "Die", etc., and making a deliberate move toward Darker and Edgier seems to have given the ghostwriters more room to breathe, giving the characters much more development and generally writing better stories. Just look at the number of Casefiles-exclusive tropes on the various pages.
Harsher in Hindsight: Considering the sheer number of stories that have been written, it's almost inevitable that this will eventually come up. One good example is Casefile #125: Stress Point. The details of the book are different (A reporter is murdered after he finds out that a construction company in bed with the mob cut corners on a new skyscraper, which makes it dangerous in an upcoming storm,) but it doesn't change the fact that the story ends with a building beginning to collapse in the middle of New York City.
My Real Daddy: While Edward Stratemeyer is the actual creator of the Hardys, all he did was create a rough idea of the character and general outlines for stories for his ghostwriters to follow. It was Leslie McFarlane, the first ghostwriter, who (after originally working on another series called Dave Fearless and finding himself disappoined at how slapdash and generic it was treated) added a lot more beyond his outline and really brought them to life. Ironic since he later grew to absolutely despise them.
Values Dissonance: The original editions, published before 1959 which featured plenty of stereotypes, particularly of different nationalities, and racist attitudes towards African-Americans. The post-1959 revised editions took them out.