Twilight and her friends in My Brave Pony: Starfleet Magic. When meeting Rhymey during his visit in Equestria, they all mistake him for a crossdressing Fluttershy. Bonus points go to Rarity, who outright states she has no problem that "she" completely transformed herself with magic into a male. The remake tries to address this by making them believe that she is disguised, which manages to make them look even dumber.
Yang has a mild case of this in React Watch Believe Yikes. She's generally a bit slower on the uptake compared to the others and is less book-smart than in canon.