When using the 'Import Articles' option to import knowledge articles, an extra '(empty)' category is visible for a few knowledge bases it may not be present into other knowledge bases.
This is expected behaviour and can be also reproduced into an OOB instance.
The reason you have an '(empty)' category in the knowledge base is because there are knowledge articles with no category set associated to that knowledge base.
It can be reproduced by following the steps below:
1. Create a 'Knowledge Base'.
2. Create a 'Category' for the 'Knowledge Base' you just created.
3. Create a 'Knowledge Article' associated to the created 'Knowledge Base' and make sure that the 'Knowledge Article' has no 'Category' set.
4. Publish the 'Knowledge Article'.
5. Go to 'Knowledge > Import Articles' from the Filter Navigator.
6. Select the created 'Knowledge Base'.
7. An '(empty)' category will be visible along with the 'Category' created.
Below is an example of how the '(empty)' category will show:
This is working as designed in order to allow you to import knowledge articles with empty categories.
If you don't want an '(empty)' category to be visible, then you can associate a 'Category' with the knowledge articles having an empty category.