I noticed a bug regarding uploading static files in APEX. When you try to upload file with same name as existing one you'll get error message that static file name already exists. But if you query apex_application_files view you can see that this file was uploaded (like workspace file). Funny fact is that when you go to static files page in APEX builder you won't see that "hidden" file.
This can lead to problems with static files in runtime because APEX sometimes uses some of the "hidden" files and not the ones you see in APEX builder. To clean up this mess you should delete files manually.
One way to do it is to use APEX SQL Workshop, but it's also easy to do it from your favorite PL/SQL IDE. The only thing you have to do is to set workspace id (security_group_id).
After that you can manage your static files in current session of IDE by using view apex_applicaton_files (or wwv_flow_files).
This was tested in APEX 4.2.2.00.11, but I know that same problem existed in earlier versions of APEX.