Black Face or Face Discoloration is caused by mod conflicts and load order issues. To resolve this you can do a number of things. Below are the list of things you should to do fix it:
A) Make sure Visions NPCs load after any other mods that touch NPCs. Please be aware that not only replacers effect NPCs. Some mods have NPC records in them when distributing armor or weapons for example. In these cases, you will need to make a conflict resolution patch. There are a number of videos on Youtube covering conflict resolution. https://www.youtube.com/results?search_query=skyrim+conflict+resolution.
B) Make sure the Visions NPCs plugin loads after any mods that may cause a conflict, such as other replacers or mods that touch NPC records. Again, see above for mod conflict resolutions videos.
C) If you have a Bash Patch (Wyre Bash), rebuild your patch. Sometimes the Bash Patch has baked in NPC records that will cause a black face.
D) Check for other patches from special tools that might also bake in NPC records and fix accordingly.
E) The most risky is to use xedit (sseedit) to remove NPC records from offending mods and remove the face meshes and face tints. I'm not going to teach you how to do this, but searching youtube should give you an idea of how to fix this.
F) If you just can't figure the problem out, head to our Discord and hit the #support channel for help. We will try to help you.
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Another cause of Black/grey face can be race records. Typically this is because you have a mod that uses skyrim.esm face data in the record, and not Dawngaurd.esm face data. This mostly affects vampires and can affect only a single race and sex.
First off this is a great AIO mod. I really love what you have done.
I was getting a gold face for all of the new Vision NPC's. I use MO2 and still had the Vision mods at the bottom of the load order (new install) and they did not show any losing conflicts whatsoever. I read through your tip sheet above (A-D) and was not able to discern anything. I then looked at the few other AIO mods that might be a problem with no success.
The solution was for me to manually move the two Vision plug-ins to the bottom of the plug-in list and set them to locked so that LOOT would not try to put them at the top of the plug-in list (which is what it was doing). Now everything works fine. Ironically the mods that were the conflict on the plug-in side were your original Pantheon mods that I still have installed (I am still working on a current play through).
Hope I did not babble to much.
Thanks for all of your hard work.