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Issues are present in Mortal Empires and Vortex campaigns (unmodded, legendary), to repeat just start a campaign.
Tower projectiles for Vampire Coast's 10 slot capitals (Sartosa, The Awakening), Ulthuan Fortress Gates and Tomb King special capitals will not get upgraded with the main settlement chain even though they do for Old World capitals and places like Lothern and Itza. Lahmia has a mostly redundant wall building chain while Khemri does not, even though both otherwise upgrade their garrison only via the main settlement chain. Black Tower of Arkhan doesn't have a way to update tower projectiles (although this may be intentional).
Skavenblight and tier 5 Skaven towers shoot Warp Lightning instead of Doom Rockets. Doom Rockets are fired by tier 4 towers, resulting in them being better than tier 5 ones.
Followers of Nagash AI is still unable to recruit Hexwraiths because it can not upgrade the faction's special building chain beyond tier 1.