One is that the Mad Titan might use the Infinity Stones to control their minds and make them tear each other apart.
Another possibility is that much like how Iron Man and Thor fought each other in The Avengers, Hulk and Groot’s fight will be due to a misunderstanding, and they’ll eventually back off on their own accord.
Of course, that doesn’t explain why the two protagonists would need to fight in the first place, but there are a few options.
As for when this fight could occur, 2018’s Avengers: Infinity War is the best bet, as Hulk and Groot, not to mention a lot of other heroes from the MCU, will cross paths when Thanos comes calling on Earth.