Since you asked.
You let them get out of control. When the assistants start getting mouthy, you should ask the head coach to help you out by controling his bench. This can serve as the warning if you feel you need one.
Then, when half the team jumps up to protest the call, you can pick an assistant and issue the T. After that, if an assistant complains about a call even from the seated position, you're justified.
Not that I've never let the bench get out of control, but I'd like to think I learned my lesson.