Basically the NPC's ignore the path grids entirely, unless they are already traversing on them. One example is near the Marie Elena, at the entrance to the residential area a gaurd may turn around to walk back up towards the temple. instead he will walk in to the crates near the ship or walk onto the ship as if trying to walk in a direct line to the door to the temple. Another example is the NPC's entering the waterfront via the tunnel will walk off the right side and into the water eventually hitting the ship as if the path grids are being ignored, and they are only interested in the package destinations.
Unfortunately I can't post my load order as of now since I'm not at home, but I was hoping someone here may have had an issue similar to this and may have insight as to a cause or particular mod/conflict that can cause this.
Also i tried to find previous mentions of this but i was unsuccessful, my search skills here are not that great.