I added a snippet that can be run (upon demand, don't activate the snippet) at Toolset > Settings > Custom Code.
I've done that, and it has cleared out the excess field groups that had been generated previously.
I navigated around in your site, including editing products, but nothing provoked generating the surplus field groups.
That's with your plugins mostly disabled.
It should be possible to re-activate plugins (product-related plugins, or plugins where custom code is added) and identify by a process of elimination which is responsible for triggering the problem.
When we know that we can see how to proceed. If it is a specific plugin that causes it, we can contact the authors and propose changes so that where they modify product-related queries they target those queries to only modify the intended ones. (They surely don't mean to modify the queries we make to check for the existence of the Toolset WooCommerce field group to know if it needs creating or not.)
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