PhpStorm version: 9.0.2
Symfony Plugin version: 0.11.109
Symfony version: 3.0.1
Template referencing works fine for template files placed under app/Resources/views but not for files placed under Bundle/Resources/views.
Here goes screenshot. As you can see there is no warning highlight at first line that references to the test.html.twig file placed under app/ directory, but it warns on templates that are placed under bundle resources. 
Code works well and bundle templates renders in browser.

Symfony plugin configuration:

I had the same issue with Symfony 3 / 4 / 5. The fix is really simple.
All you have to do is add the app/Resources/views (or templates in case of Flex) directory manually to Twig namespaces as follows:

This way you can also support custom Twig namespaces, so PhpStorm can autocomplete those as well.
If it's not working immediately, you should invalidate the cache:
File -> Invalidate Caches / Restart
                        I just had the same problem as well, however I didn't want to follow @Andrey Rudenko's answer because I would lose all my project specific configuration. Instead I followed @COil's comment and jusnt invalidated my cache and the problem was solved.
File -> Invalidate Caches / Restart -> Invailidate and Restart
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