I was able to perform filtering from both of my stacked bars in my dual axis charts that I create in Tableau Desktop 10.3.0, I have attached the workbook I created to test. The filter action is performed by selecting the value to filter on then running the action from the tool tip.
I am curious what version you are using when experiencing the issue? It might be a version specific issue.
Filter Action Example.twbx 182.2 KB