Dakari-King Mykan always wanted to make a more action-oriented story than Friendship Is Magic, to no real avail. Come the season 4 finale, suddenly the show he hates actually gets an amazing action sequence that blows any he could make out of the water (not like that's particularly hard). Irony at its finest.
Avatar: The Last Airbender fanfic The Stalking Zuko Series has tension growing between the Northern and Southern Water Tribes, with North viewing the South as uneducated yokels and the South view the North as stuck-up busybodies who didn't lift a finger to help them when they facing genocide from the Fire Nation. Then Season 2 of The Legend of Korra comes out...
The GleeGender Flip story, A Different Direction, has Faith (female!Finn) complaining about Lebron James leaving the Cavaliers in 2010; a few months later, Lebron would return to Cleveland.
In Chapter 7 of Necessary To Win, Yukari infiltrates Anzio, which, instead of Saunders, is Oarai's first opponent. In the Anzio OVA, she ends up infiltrating Anzio as well, but unlike in the fic, doesn't get caught.
Dakari-King Mykan's reasons for creating The End of Ends become extremely laughable when the finale to another one of his stories, Cyborg Davis, has an ending that's exactly like the ending to Things Change. Beat. For. Beat.
Tara Gilespie, author of the most infamous Harry Potter fanfic of all time, predicted in an author's note before Deathly Hallows came out that Harry would have to let himself die in order to defeat Voldemort, because he himself is a Horcrux. Fast forwards to when the book came out, and she was right! A lot of people had the same idea, to be fair, but the fact that Tara of all people figured it out is hilarious.
In Trolling the League, Naruto and Xanna claim to be highly advanced aliens who elevated humanity millenia ago. In an omake in the sequel Xanna runs into a human who insists gods don't exist and that she must be a highly advanced alien who elevated humanity and/or has come to soften up Earth for an invasion.