OA says that there were moldy communion wafers found at the old church, you would never find such a thing in a Catholic church that was shut down. Communion wafers are also known as the Sanctum Sanctorum, the Holy of Holies, and would never be abandoned. In fact one of the relics that was daringly retrieved when the Notre-Dame de Paris was burning were the communion wafers.
Isobel gets the phone call from Jubal alerting to the serial killers possible presence and then gets confirmation of it by hearing sounds. No trained Federal Agent would stick to a melee weapon instead of making quiet haste to a firearm in the next room with ample time to prepare for self defense like she did.