I can't assist you in the manner you require as your feedback on the issues is just on the surface, "how to fix" can't be answered if you don't feed more info.how to fix?
The auto remove depends on locks to trigger, but once triggered it rely on the other subsystems. At this point I ignore which is the cause of your problem. The only thing we know so far is that this only affects you as no one else is bringing this issue to my attention, so I don't think that it is a software flaw but a wrong provisioning on your end.
Try to debug it, and report properly. Does it happens to all uploads? Local? Remote? Deletions table? Files actually removed but CDN cached? Etc.