I recently ran into an issue where my navmesh is baking incorrectly.(see pic)
It was working fine until I set it up on a terrain instead of on a box.
I also added roughly 50-200 static game objects to the scene outside of that picture.
Here is how the baked agent is set up:
Ive tried modifying the baked agent to allow for increased slopes, even though most of this is flat terrain. Ive also tried modifying the agent radius. I haven't had any luck with either of those.
I've also ensured that all of the navmeshable game objects are marked as static as well as Navigation Static.
I saved the scene, closed unity and re-opened it. It fixed the problem