Caused by Solution of PHPBB3-11215:

Example:
Create an event listener for "core.page_header", which generates a URL like:

'U_NEWSPAGE'	=> $phpbb_container->get('controller.helper')->url('news'),

This should generate the following, at least that is what the tests for the url method say ( https://github.com/phpbb/phpbb3/pull/1102/files#diff-6 ):
phpBB/news

Note: Functional tests use another route for tests, they use app.php/news
https://github.com/phpbb/phpbb3/pull/1102/files#diff-7

However if you hover the link while being on faq.php it generates:
phpBB/faq.php/news

and so on. These pages just display normal faq.php content.

Feel free to use https://github.com/nickvergessen/phpbb3-mod-newspage/tree/develop-caitlyn for testing next time.........

Also app.php?controller=news does not work anymore.
It just says:

No route found for "GET /"

Also smilies have been broken on sub pages:
phpBB/news < smilies work
phpBB/news/topic_id < smilies won't work, as it looks for
phpBB/news/images/smilies/icon_mrgreen.gif
instead of phpBB/images/smilies/icon_mrgreen.gif

tl;dr:

1. restore functionality for app.php?controller=news
2. remove current file from generated urls (please also test form adm/index.php and stuff)
3. fix smilies and other phpbb_root_path usages while being on a non-root level
4. change extensions test to NOT use app.php/ in path