When using strftime-style time substitutions over SSH the backups fail. My guess from the backup log is that there is a missed substitution in the script as it would appear that the ls command does not have the substitution applied:
Deleting backups from /data/backups/%Y/%m/%d on SSH server [ADDRESS] older than 90 days ..
.. failed to list directory via SSH : backup@[ADDRESS]'s password:
ls: cannot access /data/backups/%Y/%m: No such file or directory
I should not that the upload works fine and that the folders /data/backups/2016/[01 through 04] exist so ls should not be failing on trying to find /data/backups/2016/01 for example.