I configured URL prefix in galaxy 18.09. It has problems of resolving some of the links, including:
     visualize -> create visualization
     shared data -> workflows
     shared data -> visualizations

I will use workflow as an example to illustrate what happens. When the mouse cursor is put on workflow, the URL shown in at the left bottom of the browser shows


But after I clicked 'workflow', the real URL shown in the address bar is actually  

Of course, there is no such a page and the browser shows a blank page. If I manually remove one galaxy in the URL, the page is correctly shown.

Beside the four mentioned above, other links work fine. If galaxy is configured without prefix, then there is no problem.

 I also tested v18.05. With all the configuration being the same, this version doesn't have the problem with prefix like v18.09 does. So I think this is a bug in v18.09 with URL prefix.