OK. I have to say that that is a substantial distance apart, for a wrong selection. I don't know how the MiPermit app works, but reviews on Trustpilot are 90% unfavourable ! Here in Cheshire East council car parks, Ringo is the app.
All I can say is that you need to investigate how the app placed the phone at one car park when it was physically at another one. These apps use GSV to position the phone, then normally tell you the car park name and then one selects a car to park, as one can have more than one on the app.
I suggest you submit reps on the basis that the app placed the car at the wrong car park, but despite this, the correct payment was made so the council did not lose any money, and clearly there was no intention to avoid payment.