I said it few times.
I think he has a problem with the message that was passed through Koeman: That he has privileges.
Before a simple training session, Koeman acting this way tells he recieved information from inside the club, informatiom Messi disagrees.
This has been something consistent with Messi, he was made at Sampaoli looking fot him in NT, he wanted Sampaoli to treat him like other players so that he won't be involved in squad discussions.
He was made when Abidal went to the media, basically calling players without naming names and putting shades on Messi.
And now, it seems our board strikes again, shifting blame on us.
Another scenario:
Messi already was thinking to leave after that 14th of August night (why always on my birthday
), this is something we already knew from the media.
He had talks then with Koeman. Koeman failed to change his mind.
So Koeman isn't the problem, but he isn't the answer.
TLDR, no. I don't think he has a problem with Koeman. For a player who seen a lot here, I doubt a 30 ,minutes conversation with new coach will make him take drastic measures.