The problem has arisen a few times, typically in custom code that is "doing it wrong", i.e. modifying all WooCommerce-related queries on certain back end pages instead of targeting their own queries, so that our query which helps determine whether our custom WC field group has been created yet or not is broken.
To be able to stop that it is necessary to identify what is doing that, which means a trial and error process using a process of elimination.
You are looking for anything that customizes the product or shop order pages. I'll provide some code you can use to clean up the excess entries, after which you can disable any plugin that might involve customizing those pages, and then re-activate them one by one, visiting the product and order pages, and checking if extra Toolset WooCommerce field groups have been generated.
If you can isolate what's doing this then we can see what can be done to stop it.
You can add the following code to Toolset > Settings > Custom Code. Don't activate the snippet, and instead run once.