Time Machine

Ok, got it. Thanks! It may be possible that TM had some difficulty in removing that particular file/folder due to corruption. Are these backups located on a Time Capsule or an external drive? If on a TC, I suggest that you perform a "Verify Backups" on the entire backup set. You can access this option by holding down the <option> key before clicking on the TM icon on the macOS menu bar. For the latter, you will need to use the Disk Utility's First Aid option to verify the external drive's integrity.

I assume you mean that you used the Time Machine interface, selected the file or folder, and then chose "Delete all backups of..." Correct? ... or did you chose, instead, just to delete that individual backup?

Have you tried control - clicking on the file to see if you get a delete option?