Seems that the stock backup is far from perfect.
Issues are regularly reported.
I prefer to use a command line tool like rsync. (Some users recommend rclone)
Probably you know it, but if it this can help, although drafty-tinkerish, here is what I’m using since years on linux systems to backup/restore:
-Have a big enough microsd formated in ext4
-in the terminal:
rsync -vaHE --force --delete --recursive --exclude=some_dir_you_want_to_exclude /source_directory/ /dest_directory/
MicroSD is mounted in /run/media/defaultuser/[some_numbers]
Use at your own risk as this can delete your data if you e.g. invert source and destination.
I was too lazy to perfectly choose the rsync options. As soon as it was working, I kept it as is. But you should look further with man rsync.
I shouldn’t but I always do this as root. If it complains about missing permissions on some files, do it as root too. (=enable dev mode in settings, login as root with devel-su)
I did put these commands in a script that is run every hour, so backup is automatic.