Views contextual filter not working for Pathauto path Im using Pathauto so set aliases for taxonomy terms. 

So this:
/taxonomy/term/1

Is the same as this:
/custom-term-url

Im using Drupals default Taxonomy term View to control the layout of the term page. This works fine for both of the paths. 

Ive created an additional page in this view with a path of /taxonomy/term/%/something and an additional filter so show different results. 

When I go to this page everything works perfectly:
/taxonomy/term/1/something 

However this returns a page not found: 
/custom-term-url/something 

How can I get my View working with the Pathauto URL?
Install Global Redirect module, this module create a unique form of all of the aliases. I am not able to test this solution of your problem But I guess it may solve the problem.