Okay I decided to dip into the land of Mods...

Got me FoMM, and like 10 mods loaded up, and a few NPCs that walk around now are walking white exlemation marks in big red boxes...

I can't seem to find what mod is causing it does anyone know off hand what could cause this kind of issue... Is it a messed up Mesh? A companion thing? any idea?

Missing meshes, as far as I know. What mods did you get, and what kind of areas are the NPCs in question in?

Yup, missing meshes. Having a <!> on random NPCs most likely means clothing, or hair mods installed wrong. Could be also guns if any mod adds them to NPCs. If you have no clothing or hair mods, open the console and click on the people with <!> and type inv, try to find out what items they have in common.

One idea is to save in front of one such person, disable all mods, then reload, activating one mod at a time until the issue is duplicated. Should be pretty easy to determine that way. Once you've got that, yeah, do what ToJKa said - could be some item is getting modified or added that is causing the issue.