During the Harry Potter parody, Deadpool points a gun at Batgirl asking what she did to the real one. That's because he's a Marvel character and aware of the Kree/Skrull War.
Superman attempts to get Ben to mock Dawn of Justice by pointing out how it's too dark and has a lack of humor. Unfortunately, these were criticisms of the new Fantastic Fourfilm as well, so it didn't help at all.
Iron Man threatens Spider-Man if they "put a teen vampire into your reboot." While they never did, Morbius is one of Spider-Man's rogues, and in some continuities, he is in fact a teen vampire.