OP, of course you were served with a PCN, your actual VRM did not appear on the CEO's database. I wouldn't read anything more into it than this at this stage.
My thoughts..
I parked and I tried to pay using the machines, but none was operational. I therefore used your PaybyPhone facility, a method with which I'm not familiar. I made a small mistake when entering my registration number - GB08ZMZ instead of GN08ZMZ. (I can see that 'N' and 'B' are adjacent on my QWERTY keyboard)
Given that I had paid to park at the time stated in the PCN, I would ask that the council exercise discretion in this instance. For information, I would also add that as displaying a ticket is optional, that is to say that motorists may pay online or 'pay and display', then the contravention description is incorrect because display is not mandatory, and indeed in my case not even possible.