Accidental Innuendo: Eric takes Henry into his room to show him his hat collection. Everything was innocent, of course, but you have to wonder why Eric's mother didn't act a bit more alarmed when she found her son with a grown man in his room.
Fridge Brilliance: The entire world is so much more wholesome than ours, the thought that Henry might be a predator doesn't even cross the mind of Eric's mom. She's only upset because she wanted Eric to make friends his own age, rather than the adults he spends most of his time with.
On the contrary, she seemed quite upset at finding him there, almost disturbed. Though the aforementioned point still stands. In Real Life, any sane adult would refuse to go into a child's house (let alone bedroom) without at least one parent in the house, no matter how innocent the intention as any parent who finds an adult alone in their house with their child would start screaming at them about calling the cops. It's a good thing reality didn't ensue.
Fridge Brilliance: The entire movie, Mahoney plays the 'air piano' and music plays. The audience assumes it's just a directorial quirk, until the end, where Mahoney realizes she does possess magic. The magic was there the entire time, but we didn't notice.
On top of that, it's cleverly set up earlier. The term 'sparkle' is used as a metaphor for the magic inside Mahoney, and in the scene where she asks Mutant about it, the dialogue goes like, "You've got that thing you do with your hands." "That's a quirk." "Quirk's not a sparkle?" The film's screenplay just became even more brilliant.
Given this store is literally magic and actively displays this nature, how come this store is not an internationally known tourist attraction with a queue of kids and tourists several miles long every day. That's because it's arguably a metaphor for all of the little miracles that happen all around us that many people don't notice. Not just that, but the store is also a metaphor for wonder. Besides Mahoney and Mr. Magorium (and Henry at the very end of the film), no adult can see how amazing the store is. Not even the woman with an octopus on her head. She looks really apathetic in the store before opening the picture book and even with the octopus on her head, she just looks annoyed and disturbed. Adults don't have the sense of wonder children do, so they have a Weirdness Censor that stops them from seeing what the store truly is.
Hilarious in Hindsight: Jason Bateman's character seems to be in a platonic relationship with the film's female lead, but there's hints that there might be something more, and you can make an argument over whether or not the two of them have potential to become a couple. Sound familiar?
Memetic Mutation: Films and TV shows love taking a shot at the film, either as something akin to whimsical torture (as in Breaking Bad) or scene dissonance (as in Brüno).