With Xabi Alonso's unbeaten Bayer Leverkusen celebrating their first-ever league title - and on course for a possible treble - Muller finished the season without silverware for the first time since 2011-12.
"We are very unhappy. We just want this season to be over and to start again in the summer," Muller told Sky after Bayern's eighth loss of the season.
"It's out of the ordinary for us to lose so many games. We'll try and put it behind us now."
Bayern, who were without the injured Harry Kane who left Germany for treatment on his back ahead of England's Euro 2024 campaign, were 2-0 up after six minutes through goals from Mathys Tel and Alphonso Davies.
Hoffenheim hit back immediately, with Maximilian Beier scoring two minutes later. Bayern were blown off the park after the break as Andrej Kramaric hit a second-half hat-trick to grab control of the match.
Muller praised outgoing coach Thomas Tuchel, who confirmed Friday he would leave at the end of the season, saying the manager "had to clean up some mess that he did not produce under not very easy circumstances."
Tuchel himself said he "had an explanation" for Bayern's troubles, but said "it's not to share with the public."
