You must change the default settings for iTunes in order for GroundControl to work reliably. This article provides instructions.
By default, iTunes will activate any connected devices. Devices remain on the “Hello” screen and don’t look any different, but GroundControl will no longer be able to supervise the devices. Devices will need to be factory reset to be used again.
Open iTunes, then open Preferences.
Check the box “Prevent iPods, iPhones, and iPads from syncing automatically.
Close Preferences, then exit iTunes.