The backup tool is interfered by GNOME's own passphrase prompt
Our backup tool attempts to unlock the volume of the inserted USB drive itself, and displays a polkit prompt stating
Enter a passphrase to unlock the volume to unlock it, but since we enabled auto-mounting of removable media (#15900 (closed), #15767 (closed)) that prompt will race against GNOME's own unlock prompt stating
Never having tested this tool or looked at its code I'm not entirely sure, but perhaps a fix would be to stop trying to unlock the device itself and instead wait for GNOME to do it? Actually, it could check if
org.gnome.desktop.media-handling.automount is set to determine what to do.
This mess was detected by the automated test suite, yay!