I've got a problem that is starting to bug me more and more as time goes by. For some reason, some of the characters in the game have different skin pigments for their body and face. For example, a black mans body and a white mans head. I've seen a glitch where this occurred on my xbox but I think that one of my mods may be at fault here . I couldn't say which one, but I suspect it may be FOOK2... The following is a list of all my mods that I have installed:
Destruction, Arefu Expanded, Project Beauty, GNR More Where That Came From, S.I.K (GNR - Sound Improvement Kit), CRAFT, CALIBR, RH-Ironsights, COMM, FOOK2, MMM, Ammo Bench, Enhanced Weather, Fellout, CASM, Reykjavik (Iceland), Alternate Start - Roleplayers, Pipboy PDA, Solace, We Jazz (plugin for COMM), F.O.W.E, xCALIBRmunitions, Existence 2.0, Pilotable Vertibird, Underground City.

Perhaps your load order would make it a little easier for us to help you.

I apologize, I didn't know if I should because it's... lengthy... But here it is:

Fallout3.esmArefuExpandedByAzar.esmProject Beauty.esmAnchorage.esmUNDCity.espThePitt.esmBrokenSteel.esmPointLookout.esmZeta.esmCRAFT.esmDestruction.esmCALIBR.esmRH_IRONSIGHTS.esmCOMM.esmFOOK2 - Main.esmFOOK2 - [[censored]] World And Neighbourhood Kit.esmFOOK2 - [DIK] DLC Improvement Kit.esmMart's Mutant Mod.esmAmmo Bench.esmEnhanced Weather - Rain and Snow.esmxCALIBR.esmDestruction - CP - Fellout.espDestruction - DLC - Statics.espDestruction - DLC.espDestruction - Main.espArefuExpandedByAzar-Radio.espS.I.K.espDestruction - Main - Statics.espProject Beauty- Broken Steel.espProject Beauty- Point Lookout.espMart's Mutant Mod - Project Beauty.espFOOK2 - Project Beauty.espFOOK - DIK - Project Beauty.espFellout-pipboylight.espCASM.espCRAFT - Activation Perk.espAmmo Bench - Remodelled.espGalaxyNewsRadio60[M].espAmmo Bench - Alien Power Cell.espAmmo Bench - Artisan.espAmmo Bench - CRAFT Plugin.espAmmo Bench - CALIBR.espAmmo Bench - Car Mechanic.espAmmo Bench - Old Ammo-Benches.espAmmo bench - Decreased Output.espAmmo Bench - Scattered Schematics.espAmmo Bench - Toolkit Retex.espFOOK2 - Main.espFOOK2 - [EVE] Energy Visuals Enhanced.espFOOK2 - [DIK] DLC Improvement Kit.espFOOK2 Main [Hotfix].espFOOK2 - Mothership Zeta.espMyFOOK2 - No [censored] Victims.espMyFOOK2 - Black & White Tranquility Lane.espFOOK2 DIK [Hotfix].espFOOK2 - RH_IronSights.espReykjavik.espCALIBR Ammo Schematics - CRAFT.espStealthboy Recon Armor - CRAFT.espAlternate Start - Roleplayers.espMart's Mutant Mod.espMart's Mutant Mod - DLC Anchorage.espMart's Mutant Mod - DLC The Pitt.espMart's Mutant Mod - DLC Broken Steel.espMart's Mutant Mod - DLC Point Lookout.espMart's Mutant Mod - DLC Zeta.espMart's Mutant Mod - No Corpse Flies.espMart's Mutant Mod - No DLC Increased Spawns.espMart's Mutant Mod - No Floaters.espMart's Mutant Mod - No Geckos.espMart's Mutant Mod - No Ghoul Raise.espMart's Mutant Mod - No Size Scaling.espMart's Mutant Mod - No Skeleton Decay.espMart's Mutant Mod - No Wanamingos.espMart's Mutant Mod - Feral Ghoul Rampage.espMart's Mutant Mod - Hunting & Looting.espMart's Mutant Mod - Increased Increased Spawns.espMart's Mutant Mod - Increased Spawns.espMart's Mutant Mod - Natural Selection.espMart's Mutant Mod - Reduced Wasteland Spawns.espMart's Mutant Mod - Tougher Traders.espMart's Mutant Mod - Zones Respawn.espMart's Mutant Mod - FOOK2.espMart's Mutant Mod - FOOK2 - DIK.esp1PipboyPDA.espRH_IronSights_Basic_PittPlugin.espRH_IronSights_Basic_PointLookoutPlugin.espRH_IronSights_Basic_VanillaPlugin.espWe Jazz.espSolace.espEnhanced Weather - Rain and Snow in Fallout.espEnhanced Weather - Radioactive Rain and Snow Plugin.espEnhanced Weather - Weather Sounds in Interiors.espEnhanced Weather - Sneak Bonus during Storms.espFellout-Anchorage.espFellout-BrokenSteel.espFellout-PointLookout.espFellout-Zeta.espF.O.W.E.- ClothingAddon.espxCALIBRmunitions.espExistence2.0.espxCALIBRmunitions_FOSEnhancements.espFellout-Full.espxCALIBR_override.espF.O.W.E.espF.O.W.E- FelloutPatch.espPilotable Vertbird by Arlix.espTotal active plugins: 107Total plugins: 114

The 7 missing "plugins" are for destruction. For some reason they cause the game to crash, they are patches for FOOK2 but are outdated.

I believe this happens if the mod containing NPCs is an .esp instead of an .esm.

I have the same issue, it's not (at least for me) only affecting modded npc's.

If I remember right, according to what I found on the forums there is no easy solution.

Edit: Ok, searched again. What I found is this: If it is mod-related you can try using FO3MasterUpdate with FO3Edit.

How do you go about doing a FO3MasterUpdate?

Edit: Nevermind, found the manual

I tried that, didn't work :-\ Also, created a merged patch.

Don't know if you made it on over to arefu yet. But the arefu expanded behaves VERY wonky when you go near certain areas. Such as the raiders location immediately outside on the bridge. I had many a crash happy FO3. Its best to save often in more than one game so in case you really had to unload it.

I think I crashed once over there, I actually downloaded Arefu Expanded because I was doing the Arefu quest and thought, why not? But the face problem has been occurring since I installed FOOK2, that's why I think it's the culprit. I'm thinking about removing it despite that fact.

I get a number of hiccups and usually I hide for the 4 day deally in a shack. Typically fixes itself. But that arefu expanded is a heads up at anyway rate. Just to save you some headaches. It does actually work all the way through though. Just tends to get crash happy. Especially if you have travelers mod.

As I said, I have it on non-modded npcs and I'm not using any "beauty" packs.
Someone wrote that it is a hardcoded bug, so I'm not sure if it necessarily is mod related.
Do a search for "head body mismatch", there was also another possible solution about adding some line to your .ini .