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).