Tagging troubles

My tagging system is a mess. The root of the problem, I think, is that the script I use to export notes from my reference manager creates groups and assigns tags to the groups and not the individual notes. The following image shows what I see when I highlight a tag:

What I want to see, rather than groups, is individual notes. I get a few individual notes because I assigned them independent of the group they belong to:

What I hope to achieve is removing the tags from the groups, but retaining the tags for the notes contained in the groups. I have tried removing the tags from the group folder, but it also removes the tags from the individual notes.

Also, is it possible to have parent tags show notes that are assigned to the child tags? Right now when I click on a parent tag, there is nothing:

I only see the notes when I click on the child tag:

It would be very useful for me to see notes when I click on parent tags.

Any help is appreciated!

Just a quick update. I solved this problem for creating future notes from the script by editing the script to tag the notes instead of the group. However, I am still interested to find out whether there is a solution for removing tags from groups but retaining the tags in the notes contained within the group.