I agree about this not being a Query Wrangler issue, though I just wanted to throw this out there just in case anyone else ran into the same thing.
I also had a number of custom post types and had been using custom link structures (I happen to be using Types).
If the post type that I was filtering used the same url that the Query Wrangler page was using, the additional pages from the pager would give me a 404 error as well.
For example, I had the structure ‘site.com/products/product-name’ for a Product content type.
If I also had a basic page with a query using the url ‘ site.com/products’
‘site.com/products/page/2’ etc. would give me a 404 error.
Changing either the Query page url or the structure on the post type fixed it.
