You need to separate out groups, branches or parent/child tags into separate custom taxonomies. In general, you can use a particular Taxonomy, such as Product Category, (or Category/Tags, each Taxonomy and each Custom Field) only once in the form. This post tries to explain this a bit better (you can use a plugin to switch category terms from category to any new taxonomy that you make, so it is not so hard to do). It is a really awful preachy lecture I wrote:

https://support.searchandfilter.com/forums/topic/multiple-categories-combination/#post-55166

Sorry about the tone, but the message is right and it links to good plugins (except taxonomy switcher I think).