Today I ventured to Primm and noticed that people have missing textures and red exclamation mark on them. What could possibly cause this? I also had this problem before but then I was using Interior Lighting Overhaul without required DLC.

Some screenshots: https://onedrive.live.com/redir?resid=130B665BF39DFD1!6531&authkey=!AH13TZHgYl18-V4&ithint=folder%2C

My load order (I've hidden all messages and CRCs) - most, if not all mods are updated to the latest version:

FalloutNV.esmDeadMoney.esmHonestHearts.esmOldWorldBlues.esmLonesomeRoad.esmGunRunnersArsenal.esmClassicPack.esmMercenaryPack.esmTribalPack.esmCaravanPack.esmNVInteriors_Core.esmInterior Lighting Overhaul - Core.esmInterior Lighting Overhaul - L38PS.esmoHUD.esmNew Vegas Redesigned 3.esmFCOMaster.esmGomorrah Redesigned.espNVInteriors_Urban_Edition.esmNevadaSkies.esmPerkEveryLevel.espAdvanced Recon Range Finder.espThe Mod Configuration Menu.espCentered 3rd Person Camera.espMission Mojave - Ultimate Edition.espImproved Throwing1.espEVE FNV - ALL DLC.espCamp Searchlight HotFix.espImmersive Karma.espImp's Timescale Adjuster.espdD - Enhanced Blood Main NV.espRX-Auto Incremental Save.espInterior Lighting Overhaul - Ultimate Edition.espILO - Nevada Skies Patch.espMMUE POP.espMMUE-CP-EVE.espFCO - GlowingOne.espVurt's WFO.espNew Vegas Redesigned 3.espCass alternate version.espMMUE-CP-NVR3.espCompanion Sandbox Mode3.espMMUE-CP-ILO.espFNV Realistic Wasteland Lighting - Full.espNevadaSkies - Ultimate DLC Edition.espILO - GS Shack.espMojave Nights.espILO - PipBoy Light.espZan_AutoPurge_SmartAgro_NV.espTotal active plugins: 48Total plugins: 54

Those aren't missing textures, they're missing meshes. Something is not installed properly.

PS: looking at it again, I see that it's their heads that are causing the issues. So it's probably a mod that makes changes to those.

Yes, only heads have issues. I remember having updated Fallout Character Overhaul to 2.3.1 (not from 1.x) recently.