Is it permissible to watch anime that contains a few scenes of shirk (polytheism or idolatry) while avoiding watching those specific scenes, knowing that the anime's main content is not related to shirk?

It is not permissible to watch cartoon films that contain polytheistic expressions. However, if it is possible to watch the permissible ones among them and avoid the rest, then there is no harm. Nevertheless, it is advisable to refrain from them due to their waste of time and limited benefit. One should utilize their time in what benefits a Muslim in their religion and worldly life.