Products not linking to the right subcategory

[rapidmedia]

Research indicates this is due to:
toplevel/category1/pfd
toplevel/category2/pfd-1
toplevel/category3/pfd-2

and

toplevel/category1/subcategory1/pfd
toplevel/category2/subcategory1-1/pfd-1
toplevel/category3/subcategory1-2/pfd-2

Disabling SEO fixes the issue. Some products don't follow the proper category tree and default to a particular category like pfd-1.

Any solutions or possible ideas that fix the problem and allow SEO to be enabled?

Joomla3.4.8
VM3.0.14
Custom Filters Pro 2.3.1

[Ghost]

Are you talking about "back to category" button?

[rapidmedia]

It's a URI/category link issue. Say I click on a multiple category product displayed in a product list for toplevel/category1/pfd, the product details page is for toplevel/category2/pfd-1. Colours and template should be for category1 not category2. I've read that having menu items associated with category1/2/3 and pfd/1/2 can cause this issue as well but there was no effect when I removed the menu items.