I have a weird issue with the mannequins collision box, for some reason while in game they move a couple of feet in front of where the collision box should be and then the mannequins themselves have no collision, it gets rather annoying running into invisible blocks, the creation kit shows nothing is wrong.

That is the mannequin bug. I am hoping it is getting fixed with the navmesh bug as I use lots of mannequins. Go to where the mannequin is suppose to be and find the activator. Activating them usually forces them to return to the xmarker for a while anyway. Be sure they are on the navmesh, that the activator is not facing 0.000 on the z axis and you could try adding one of the custom scripts. SLuckyD's Vanilla Mannequin Script Fix seems to help, but does not completely eliminate the problem.