2006 Scion xA with 151,000 miles. No major work besides two tune-ups (which includes the one I mention below) and a fan blower replacement.

Several weeks ago, at idle, the CEL came on and the engine started sputtering, shaking, and accelerated poorly.

Took it to my mechanic and they replaced the I.Coil # 2 and the sparkplugs. Several days later, the issue repeated in the same manner.

I took it back to the shop, they did a warranty replacement on the coil. Several days later, the light came on and the issue repeated. After a few hours, it operated normally again. I took it back to the shop, and because nothing was happening when I dropped it off, they had no answers for me. Well, today, the car was running fine in the morning. I left work for lunch in the afternoon, and the issue occurred again! I just tried starting it and I don't have the same problem.

I am going to try cleaning to MEC tomorrow because it seems simple, but now I don't know what else to do if the issue keeps occuring.

 

Next time it throws a CEL have the codes pulled at an Autozone or other auto parts store that does it...that'll at least give somewhere to start looking and would likely show which cylinder is misfiring if it's a coil pack. You can swap the coils between a 'good' and 'bad' cylinder, clear the code(s) and see if the misfire 'follows' the coil pack in question.

I highly doubt you've gotten two bad coil packs from the shop. Codes will go a long way in troubleshooting your issue.