No. A team getting penalized for 12 men on the field one time is not enough to disqualify a HC. If it was, there would be no HCs because it happens to every coach at one time or another. It's an issue when it's something that consistently happens and you can't know that from one game.
In addition, it's usually the responsibility of the HC to call timeouts and some HCs don't want anyone but them calling them. Finally, the players should be counting when on the field an the Lions staff was telling them to get someone off so it's not like the coaching staff didn't know it.