Hello,
Can you check your "Including sub categories" option in your Filter Configuration ?
Second step to check, in your HikaShop filter module, in Extensions => Modules, click to edit your HikaShop Filter Module, look for Menu option, do you have like this screenshot example, if you have the menu item id in order to your filter look 
IN this item menu.
If this option is already setted on "
Yes", there is something strange and so, the best way to progress will be to send us 
back end references via our 
	Contact us
 form, just add an 
Url link to this topic.
Awaiting news from you.
Regards
Awaiting news from you