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As of patch 1.6, if you modify a vanilla race in any way (it could be as simple as removing a spell) the race's 1st person model will fail to render in-game.
As of patch 1.6, creating custom armor is completely broken. While it may seem normal in the CK, in-game the armor will fail to occupy any body slots and thus the NPC(s) will instead be walking around naked. This will also happen if you modify vanilla armor, or have a custom armor item using vanilla meshes.
Patch 1.6 has introduced a critical bug relating to dialogue. Attempting to modify vanilla dialogue in any way will result in it becoming completely broken, with the audio and lip sync failing to work. It also causes any attached result script to fail to function. This is a very serious issue which affects almost all CK users.