Followings scrape > unfollow is no different to database scrape > unfollow
GOTO UNFOLLOW tab
UNCHECK "bot follows only"
Set all other options as normal
As to why this happened, it could be an old bug that has long since been fixed if you have had the program for a while. Or it could be something else.
But take regular backups, at least weekly, also a weekly submit logs:
HELP > LOGS > SUBMIT
Then if it does happen again, there will exist all the data required to look deeper into it