I actually have the same exact problem. Mines is also with the qbittorrent application, though it seems to be inconsistent. I'm using 3 instances of hotio's qbittorrent-vpn with 1 being the latest version and 2 running on 4.3.9 and I only have this problem with one of the 4.3.9 instances.
If I exclude folders from appdata backup does it still shut off the containers that are associated with those folders or does it keep them on?