So I’ve seen some things that seem like anomalies in my current game.

1. As I added cities I was building Clerics and then Bell Towers.  Eventually after a few cities I was unable to build Clerics in my new settlements.  After a war in which I captured and razed a few opposing towns & forts my settlements were able to build Clerics again.

2. I built the Tower of Dominion in my first settlement.  However just recently I’ve seen it listed as something I can build in a Town not too far from my first settlement.  Not sure it’s connected but I just captured and razed a major enemy town that may have had their Tower.