Listen to recordings of outstanding ensembles in order to train your ear for what a "good" band sounds like.
Don't be afraid to isolate sections and have them play a section when something doesn't sound right. Sometimes, you just have to go into a "search and destroy" mode.
Critical listening and having the ability to pick out mistakes at a high level is a skill that takes time to develop.
The basic building block of every great ensemble is good tone quality. When you get to the heart of that, the other things are much easier to deal with because they are so much easier to pick out of the ensemble sound. If you have multiple sections playing with poor tone quality and intonation, it can be overwhelming to figure out where to start.
Where are you located? Maybe there are some fellow yellowboard contributors in your immediate area that might assist you.