Insist that students play in tune.
I know that seems obvious and trite, but as a young director I had bands that struggled with tuning and intonation. I asked the same question you did to some wiser directors and got the answer above. So I went to work demanding that each student know how to play in tune, how to manipulate their instrument according to the tuning tendencies of their instrument and stopped rehearsals when pitch went nutty.
I also bought, read and used the book, "Tuning the Band and Raising Pitch Consciousness" by James Jurrens, edited by Richard Han. It's an RBC publication that should still be available.