Toy Ship: Dinky is implied to have a crush on Pipsqueak.
Some between Alula and Pipsqueak as well, though with more Tsundere.
I Knew It: Many people in the comments guessed that Princess Celestia was the one who was replaced by a changeling in "Wedding Bells Bug Hunt". Some even guessed the changeling was Chrysalis herself. DING DING DING! We have a winner!
The Unreveal: Trinary tried to built up the above as a huge twist, but ended up making it just obvious enough that readers were able to guess it, which may or may not have ruined what Trinary was going for with it.