Backupninja is frozen because a command is waiting for an user input but Backupninja does nto report it.
To fix this failure, just run the problem command manually.
In my case, the message was:
The authenticity of host ‘<…>’ can’t be established.
SSH-RSA key fingerprint is 13:62:48:38:a5:10:84:a3:0b:14:2a:ad:c2:15:c2:d1.
Are you sure you want to continue connecting (yes/no)? yes