Accuracy can be greatly effected by a number of factors as you said. With each new iPhone that has come out the GPS chip has been more accurate, so if she was using an old iPhone 5 it could perhaps having worse accuracy. However, I have never seen issues with accuracy and many users have commented about how excellent and accurate Cachly is.
You can tap the current user location and it will show what accuracy you are getting from the GPS. I just tested it and was getting +/- 5 meters.
Cachly uses MKMapView location updates for the green current location indicator. We also use the standard CLLocationManager with kCLLocationAccuracyBest and kCLDistanceFilterNone for various places in Cachly. These are all turned off on non-map screens to save battery.
It would be hard to know specifically why that user felt that Cachly wasn't accurate, but if they were comparing it to a GPSr then it would be no comparison. The chip in the iPhone cannot compare to that.
I haven't seen this either, but I guess I have never hopped out of the car and gone running for a cache. My caching involves helping the kids get out of their car seats and getting them ready to go before we can go looking.
What iPhone do you use?