I live on the opposite coast but the same kind of crap happened to me a few years ago.
I was stopped at a T intersection (3 way stop) and saw the cop sitting in his car pulled over on the side of the road to my left. I looked him in the face, stopped at the sign, and proceeded.
He pulled me over, said I ran the stop sign, and almost ran over a pregnant woman. There was no one else in the area unless she was invisible. I said what woman? He said she just went into her house... riiight.
I went to fight the ticket, and in court they said did you stop? I said yes. They said what is your definition of a stop? I said all my wheels and tires were completely stopped and then I began. They said for how long? I said at least a second. Then the cop interjects, PA law requires 3 seconds as the minimum length for a full stop. So based on that, you could stop completely for 2 seconds, and it is considered by the law you didn't stop.
They offered to drop it to "disobey a traffic control device" to eliminate the points. I still thought it was major BS but figured I am never gonna get off scott free (they want the money) so just suck it up to road tax. Afterall, regardless of what you admit here, we both know you probably break driving related laws every single day. Sometimes the universe dings you unfairly but in the end you probably get away with way more than you are caught for.
My advice is fight it, without a lawyer, hopefully they drop the points, and move on. Good luck.
05 S4 4.2 6 spd
07 A3 3.2 - Wifey's