Funny to see this come up. I had this happen last weekend in a 6th grade girls game.
Early in the game, I thought I heard an assistant complaining about a no-call, but since I couldn't tell for sure without turning my back to the play, I let it go. Later in that quarter, an assistant clearly complained about what he thought was a missed travel, so I issued a bench warning. The head coached asked who it was on, so I replied, "The assistant complaining about the travel."
The HC tried to tell me the comment was a discussion between the coaches, but I wasn't buying it. I let the HC know assistants don't get to complain about the officiating. The message must have been loud and clear; I had no issues for the remainder of the game.
