According to him, Messi had a problem with the club, which has now be sorted out.
The 33-year-old tried to force a move away from the Camp Nou this summer, citing an exit clause in his current contract.
Messi eventually made a u-turn, backing down from taking Barca to court.
He also gave an interview, where he was critical of the president, Josep Bartomeu and the board.
“That all went over my head. That was a dispute between Messi and the club.
“I have spoken to Messi since then and we are back to normal and continue to work with each other,” Koeman told Fox Sports Netherlands.