Prius (2004-09) :: Engine Will Not Stop Idling And Idles Rough

Just picked up my 2004 Prius from the Toyota dealer body shop. The driver's side was scraped by someone who wanted to be in my lane. Fortunately, we were only going 35 mph. The rear door skin had to be replaced, and most of the side had to be prepped and painted. There are a few silly mistakes: they forgot to replace the driver's door plug, forgot to replace a lower clip, and smudged a tiny area new paint on the bumper. I brought that to their attention and they are going to take care of it... they have to order the plug and clip.

However, as soon as that conversation was complete, it was time for them to close shop. I sat in my Prius, started it, and the check engine light was on. Wasn't on when I dropped it off for the repairs. Also, on the way home, I noticed the engine wasn't turning off when I came to a complete stop (even though the animation says it was off). At idle, the engine is also rough. Looked at the charge bars, and well, there were only two bars showing.

I thought perhaps, though it's not done this before without the animation screen showing it, the engine was on merely to recharge the traction battery. On the way home, the traction battery returned to full charge (green), but the engine still was not turning off when the vehicle was at a complete stop... not was it turning off when coasting... and when arriving home, even with the car in park... and still idling rough. All the while, the animation on the screen is indicating the engine should be off.

When I replaced the traction battery three years ago, I also replaced the 12v with an yellow top Optima. I wouldn't think the Optima is already going bad. I also do not believe in coincidence. I wonder if perhaps some bad fumes have tainted the MAF, or who knows.