This has been happening for a while. These are the steps to recreate

1. I have a document library that is no longer inheriting permission from the parent site.
2. I give editing permission to a group in this document library.
3. I then see that this group has also been added at the parent level with editing permissions.
4. I delete group from the parent level.
5. Group also gets deleted from the document library level.
6. Re-add group to the document library with editing access.
7. Verify that the group did not get added at parent level again and it has not.

Any idea as to why this happens and how to stop it.

This has been happening for a while on our SharePoint Online Site. These are the steps to recreate:

1. I have a document library that is no longer inheriting permission from the parent site.
2. I give editing permission to a group in this document library.
3. I then see that this group has also been added at the parent level with editing permissions.
4. I delete group from the parent level.
5. Group also gets deleted from the document library level.
6. Re-add group to the document library with editing access.
7. Verify that the group did not get added at parent level again and it has not.

Any idea as to why this happens and how to stop it.