The Bavarians were slumped to a 1-0 defeat courtest of a late goal at St. Jakob Park, leaving them with the difficult task of having to win by two goals against the plucky Swiss outfit in the second leg to advance to the quarter-finals.
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Muller, who came on as a substitute, and Badstuber felt that the 86th minute goal by Valentin Stocker would have been avoidable had the other tracked Jacques Zoua in the build-up to the winner.
It has now been confirmed that the two exchanged angry words in the wake of the match with the rest of the squad looking on, only for Heynckes to break the duo up.
"There was a disagreement between the two players, but things are perfectly fine now," Heyncked told Bild.
Bayern playmaker Toni Kroos implied that it was an isolated incident, and one that should be quickly forgotten.
"That happened in the dressing room, so I think it would be best for it to stay there."
Bayern welcome Schalke to the Allianz Arena on Sunday for a mouth-watering clash between third and fourth in the Bundesliga.