Does your extension take into account simple product attributes if this product is assigned to a bundle or group product?
Default Magento has quite a specific feature: navigation displays not only the attributes of bundle/grouped products, but the attributes of the associated simple products as well. Our extension doesn't conflict with this feature, so it won't fix such behavior, unfortunately. However we have a little life-hack for you (which will work with and without our extension enabled).
Let's consider "Manufacturer" as an example attribute. You can create 2 separate attributes: the first attribute for simple products (within bundle/grouped products) as "Manufacturer (not visible)" which you'll set as not used in the layered navigation. And the second attribute for bundle/grouped products as just "Manufacturer", set it as Filtered (with results).
This will help customers avoid confusion when searching your store. To improve the UX further, you can set up Magento 2 Elastic Search. It also offers search by attribute, but the number of these attributes is much bigger. The two extensions are compatible.
See more details on Improved Layered Navigation for Magento 2 page