I am playing on the PC. If you have discovered the locations, look at your map. At -4086,1766 is a safehous labeled Angeras Church Safehouse with no church icon. At -3315, 3395 is the Angeras Church Icon but it is next to the Sillavik safehouse. I noticed this since I just discovered the Sillavik safehouse inside of a church, but the message upon approaching said 1/1 weapons found 100% complete. I think this is from the other safehouse to the NW. Both of these locations are in the South Coast region.
AngerasChurch|690x388 AngerasChurch2|690x388
I am on a single player game with no one else. Specs of PC are not related to this problem. As a side note, the columns in the churches with the apses in them can be walked into from the side away from the center of the church. This is a clipping problem I have seen on many churches with the side apses.