I noticed this too, there is no way to only choose a subset of a directory, Once you choose a directory everything under that directory will be backed up. My choice has been to pick and choose what I want to backup carefully.
What I can suggest is to lessen your full or incremental backups, it should purge out the data. If you don’t want to do that, then remove the backup, and choose less to backup for the client. It should purge what you don’t want. I am very hesitant to directly delete anything in the backup destination. It looks like the system uses junction points excessively and any deletion can have unexpected consequences.