I am calling setFocus on a QGraphicsItem while its scene does not have focus. If the scene gets focus, it sets focus not on my wanted item but on the item which had focus when the scene lost focus.

This happens in my pyqt project, so no C++ example.
But if you grep for passiveFocusItem in the qt source it should be clear what happens: passiveFocusItem is set when scene loses focus. Next I do setFocus on the item which does not change passiveFocusItem. When scene regains focus, passiveFocusItem is used.