(Edit: No real need to have folders of brushes in defined folders that you added to the Gimp path. Works just as easily adding the folders to the regular Gimp brushes folder. Just added complexity but up to you.)

Some time you tagged one or other of the brush set.

Example: Two folders of brushes sponge and zigzag. Both appear in the filters section.



...but if I filter by sponge the zigzag brushes show as well.



If you go into your Gimp profile (for Gimp 2.8 that is ~/.gimp-2.8 ) and look in tags.xml those zigzag brushes are tagged sponge.



You can go though and edit out those tag entries.
If you are not bothered about any tags you might have set, the easiest way is delete the tags.xml file. Gimp will make a new default file without any tags.