It first happened to me during my first weekend with the car - 2013 GT manual. It's been back to the dealer four times now. The first time they couldn't replicate the issue and just cleared the codes. Don't remember what they did the second time I brought it in. Third time, I told them to take it out and really get on it and they were able to see the flashing CEL. They did the CPS relearn and, for a while, I thought I was good to go. Fourth time it happened, they swapped the CPS, but that didn't fix the issue. They had a Field Service tech come out to take a look and determined it was a programming issue, did a couple of data logs, and sent the info back to HQ.
I had read up on other posts here and other forums, and it seemed that most folks just needed to do the crank position sensor relearn procedure. I figured it was a band-aid fix once I saw that some had to do it every few months. I've had my car back for a couple of weeks now and haven't heard anything yet.
Black 2013 5.0 Manual, Boss H-Pipe and Side Exhaust, Borla S-Type AB