You should probably watch the sequence again. IIRC he was basically done with the stop at that point when he asked her to put out the ciggy.
I did see the sequence, but as I said, her hostility triggered a red flag and prompted him to talk further with her. She was still legally detained so the Trooper had the right to ask her to put the cigarette out for his safety and to determine if the cigarette was being used to mask other smells.
Have you seen the film where he has her down on the ground? for not using her light for a lane change.