gmakhs that's a really good clue, it probably means either backups aren't completing correctly or deduplication isn't working correctly.
If backups aren't working correctly then you'll probably see folders in /backups/site-id/ that look like /wip-snapshot123/, instead of just /snapshot123/. The WIP (work in progress) could be failing for many various reasons, some things I would check is if the database dumps are present in the WIP folder.
You can check how many WIPs you have:
find /backups -maxdepth 2 -type d -name "wip*"
If you need to delete WIPs to recover some space:
find /backups -type d -name "wip-snapshot*" -exec rm -rf {} +
You mentioned manual backups working, so my guess is you're actually having dedupe problems. The first thing I would try is going in your control panel settings to service>backups and try toggling the retention date to something older, wait a minute, then toggle it back. If backups are running fine and it's just old backup cleanup not happening, this might fix it.
You can run this backups tester too, see what it says:
bash <(curl -ks https://api.cpfence.app/backup_test.sh)
Are you still on BTRFS for your storage drive, or did you switch to EXT4? I had dedupe problems too, which went away after switching. @xyzulu posted a great fix to convert EXT4 without rebuilding the whole server, just copies the necessary file structure and then reformats the drive and then puts the file structure back, it's pretty easy, 9 commands:
$: sudo systemctl stop appcd
$: find /backups -mindepth 1 -maxdepth 1 -type d -exec stat -c "%n %U %G" {} \; > folders.txt
$: sudo umount /backups
$: sudo mkfs.ext4 /dev/nvme0n1
$: sudo mount /dev/nvme0n1 /backups
$: echo "/dev/nvme0n1 /backups ext4 defaults 0 2" | sudo tee -a /etc/fstab
$: awk '{print $1}' folders.txt | xargs -I {} mkdir -p {}
$: while read folder user group; do
sudo chown "$user:$group" "$folder"
done < folders.txt
$: sudo systemctl start appcd
Just check lsblk to fix where your backups folder is mounted (/dev/nvme0n1, etc). If unmounting fails because backups are running or other, you can force it:
sudo fuser -cuk /backups
sudo umount -l /backups
