I'm having the same issue a couple others mentioned, with exterior chapel windows showing up as bright pink, or red, or yellow. Haven't checked 'em all, but I found that to be the case in Bruma, Cheydinhal, Bravil, and Leyawiin.
I have Better Cities, so made sure to get the relevant patches, but it doesn't seem to fix that issue (deselecting the patches in data files doesn't fix it either, not that it would make sense for it to).
And I am also experiencing a conflict just outside the Bruma chapel main entrance, with the stairs covering part of the doors there. The BC Bruma patch doesn't seem to solve this.
Otherwise, the mod is excellent - very atmospheric, nicely-written dialogue, and tons of character. If I could just get rid of those bright, candy-colored windows it would be perfect!