Misfire after thermostat replacement?

I had a code come on to replace my thermostat. It broke open when driving in colder temperatures it came on and my heater stopped working. I needed to drive an hour away so today I took it in to a shop to have it replaced. They replaced the thermostat and replaced the coolant. They flushed the radiator and reset the computer. The light was off, I drove off and by the time I got to a red light the Check Engine Light was flashing and when I stopped the car shook. I took it back and the light is now solid and read cylinder 3 misfire and the shop said to ignore it just drive it and it will go away.