Kermit is the only regular Muppet to appear in the movie, unless you count Statler and Waldorf's cameo at the movie theater.
During the outtakes before the credits when Kermit is trying to pull Croaker in a locker and keeps getting his hand caught the locker next to them opens showing a poster of a rainbow with the word "Believe" on it as a nod to the song "Rainbow Connection" from "The Muppet Movie" which is another origin story of Kermit when he and the Muppets came to be. The song was revived again for the movie "The Muppets" when the Muppets come back after so many years of being away.
When Pilgrim, Croaker and Kermit are chasing after the truck and Kermit trips, he is helped up by a teenage boy. Afterwards the boy is opening the mailbox you see the mailbox says Henson on the side as another nod to the creator of the Muppets Jim Henson.
The red pickup truck that takes Goggles and Blotch has the license plate JMH 924. This is to recognize the Muppets creator Jim Maury Henson (JMH) whose birthday was September 24, 1936 (924).
The name Professor Krassman has been used in another Muppet movie. In "The Muppet Movie" when Doc Hopper has kidnapped Kermit and Miss Piggy he has brought a German scientist Professor Max Krassman played by Mel Brooks to give Kermit a lobotomy with his machine to make him do his television commercials. However in this movie this Professor Krassman's first name is Hugo.