Is it permissible to benefit from the papers and pens that the father brings from his work, knowing that they are not rightfully his and that this provokes his anger?

If your father obtains things from the center legally, from the authorized person, then there is no harm in you benefiting from what he gives you from them. However, if he took them without right, then it is not permissible for you to accept them or benefit from them, and they must be returned to their owners if they are known, because accepting them makes you like an usurper, and what is unlawful does not become lawful.