First thing that comes to my mind is that Antioch and Damascus already have other guild houses in them so IIRC it is not possible to have another guild in them. Other than that, I am pretty sure there are some bugs involving guilds. In my latest game with Milanese, I just conquered Venice and got offered a Master Thieves Guild there. The strange thing was I did not have any level Thieves Guild in any place in my Empire and even stranger was that Venice did not even have a brothel to begin with.