What is the ruling on dealing with a mosque built for Salafi doctrines, which later turned out to be supervised by a Sufi group and has a grave adjacent to its mihrab?

The agent's action of building a mosque in a manner that contradicts the principal's instructions is a clear error. The agent is a trustee bound by what he has been authorized to do, and his contravention necessitates liability. His action is not enforceable if he acts contrary to instructions. What your friend did by building a mosque for the Deobandi group is an error because he was among the Ahl al-Sunnah wa al-Jama'ah, and the Deobandis are not upon the methodology of the Salaf. The presence of a grave outside the mosque does not cause harm if there is a wall between it and the mosque, provided that the mosque was not built for the sake of the grave.