Stolen from Glitchfinder's JP Navmesh Update:
Ever found yourself building at most settlements, only to realize the settlers weren't the sharpest tools in the shed? Trying to walk through benches, running around the settlement rather than through it, and generally just not really understanding where they could walk? Turns out most settlements need some real work.

The main issues are precuts, areas missing navmesh, navmesh below terrain and navmesh poorly shaped. 

Precuts: objects that can be scrapped or moved get a special navmesh under them to prevent NPCs from moving thru them, this is called "pre-cut". When you scrap or move those objects the navmesh under them opens up for NPCs. Most precuts in the game were autogenerated and have poor shapes creating delays to NPCs navigating the space. Also most exterior pre-cuts where much larger than the objects they were under to the point where large sections of settlements would be un-navigable by NPCs, until those trees, cars, etc were scrapped. Lastly, a lot of objects that are scrapable did not get precuts at all.

Areas missing Navmesh: A large variety of objects/sections are missing or deliberately did not get navmeshed, these include: Large rocks/Cliffs, small/low rocks, hill edges, ramping terrain, fallen logs, junk or trash piles that are low to the ground, so on. When remeshing these I do not do objects with more than an apparent 30 degree ramp up, or large protruding objects BUT honestly there is no reason that logs parallel to the ground should not be navigable. Also many of the high to low sections like cliffs and hill edges can get something called an Edge Portals, which I call jump-downs (as that is what the NPCs do when they use them), so I mesh those cliff/hill edges so the NPCs will actually use them. Many of the hill edges were setup that only flyers would use them, as far as I know flyers will use those Edge Portals to go up.

Navmesh below terrain: A large part of the navmesh in most exterior cells is below the terrain itself. Sometimes it is not very much and the pathing AI can handle it, other times its a massive difference and the AI fails badly. Rocky cliff areas have the worst of this I have seen so far with mesh several feet below the surface, but if you look at a before image (I try to post a before and after for each of these), you will notice massive sections of road and ground that are below the red triangles that make up the navmesh.

Navmesh poorly shaped: So the autogenerated navmesh (especially the precuts) make weird elongated shapes that the NPCs will hesitate or act drunk or spin around using. While the transition sections thru doorways and changes in elevation can have narrow triangles (I do this myself) these are sections that the mesh must use the narrow triangles. Autogen mesh with create primary paths where it is not uncommon to have an elongated triangle 1/3rd the length of a cell (roughly 100 feet) and less than a foot wide, that is a triangle with dimensions 100 x 100 x 1... and it normal to have several triangles like this stacked!