Hey everyone! I Think i found a solution and honestly is the most simple thing.
1: Login to your wordpress admin panel (www.YourWordpressSite.com/wp-admin)
2: On the left hand side go to Settings > Permalinks
3: Scroll all the way down to the bottom under ‘Product permalink base’ from here you can select one of the premaid links or select a ‘Custom Base’
4: If you selected to use a Custom Base you need to have your shop directory in part of it for example this will NOT work /%product_cat%/
the reason this will not work is because it is missing the shop directory. To make this one work for you would need to do this /shop/%product_cat%/
this would work because it contains the shop directory.
Thats basically it. You dont need to have the same thing i have, /shop/%product_cat%/
, you can also change after /shop/
to whatever you want to make it more customized. Hope this helped! Fixed my problem i was having!