I've only ever seen this happen in my game to mod-added NPC's which have been created with their size and weight lower than 1 and 100 respectively. When body mods like CBBE are applied to the smaller size it causes an issue where the head loads incorrectly relative to the body. All I do is open the mod in the Creation Kit, select the NPC in question, change weight to 100.00, save, and reapply the facegen data (select NPC, ctrl+f4, yes, yes to all) for good measure (this last bit can also be used to fix gray face), save again, just because I'm really anal, and bam. Works every time. Or, like, the two times I've actually had the problem, but still.