In the following clause the agent is in the accusative, not ablative. Why?
quod Civitas Aquilegensis et oppida Sancti Viti A. et Sancti Danielis in dicta patria consistentia cum omnibus eorum districtibus, pertinentiis (…) habeantur per ipsum Reverendissimum Dominum Cardinalem et Patriarcham
(the full sentence is too long, you can read it here)