It seems my gresource.xml was wrong

Wrong

<?xml version="1.0" encoding="UTF-8"?>
<gresources>
  <gresource prefix="/com/example/app/css">
    <file>css/style.css</file>
  </gresource>
</gresources>

Correct

<?xml version="1.0" encoding="UTF-8"?>
<gresources>
  <gresource prefix="/com/example/app">
    <file>css/style.css</file>
  </gresource>
</gresources>

According to the documentation I shouldn't subpaths are to be put in th <file>subpath/file.ext</file> tag not <resource prefix="../subpath"></gresource>