Brando was a certified flake...but a magnificently talented actor.
A number of his portrayals were pure genius.
Seems Marlon thought Kilmer was practicing a scene which had him impersonating Brando's character(which sounded alot like the real life Brando) a little too enthusiastically.
In spite of Kilmer's attempts at reconciliation Brando refused to speak to him for the rest of the production.