What is the legitimate Islamic ruling regarding an extra amount of money I received due to a software error, and royalties that have not been paid to their rightful owners, knowing that I have outstanding dues from the company that I have not received?

You must return the money you have to the company and demand your monthly bonus and end-of-service bonus from the company without betraying the trust, for Allah Almighty says: "Indeed, Allah commands you to render trusts to whom they are due," and for the saying of the Messenger of Allah, peace and blessings be upon him: "Render the trust to the one who entrusted you, and do not betray the one who betrayed you," and "Take your right with dignity, whether it is given fully or not." If the company does not acknowledge your right, then the ruling will be for the judiciary.