For example if I have a php script called "RunAllTests.php" in '/var/www/tests/RunAllTests.php' and I execute phpunit within the that directory, the includes in "RunAllTests.php" are found.
If I execute phpunit on that same file, from another directory, lets say '/var/www/', the included files in "RunAllTests.php" cannot be located. - "failed to open stream: No such file or directory in"
I kept this a little bit vague, let me know if you need some more specifics.