Ensure your category has the correct menu ticked in the section "in which menus should this category appear?" 

Your category will not show up if it is not in a menu.

You might find during the sync that the system has pulled over 'Categories' you have no intention of being available to sell online eg 'Staff Menu'.  These can be easily removed from WOWAPS by unticking them in your Lightspeed online menu:

Only the selected categories will be synced and shown in WOWAPPS.

You can have this category available for online "takeaway" only or available for "Dine in" which would be visible using WOWAPPS QR codes.