Right now unit tests (php at least) are associated by name with the file they're testing against.  This works nicely in most cases but in at least Zend Framework you can easily have several of the same named controllers that you want to test against (ie IndexController).

This means that things like navigation and code coverage aren't generated right because it doesn't know what test case to use.

To get around this it would be either nice to manually link up a test case with a file or, perhaps better, to take in account the directory structure of your test folders and not just name.