Currently using 4.3.46, where we noticed that a lot of PointOnEdgeExceptions are being thrown. Upon investigation, I found that this happens whenever a NavmeshCut component is updated and the resulting position overlapping with another NavmeshCut, the navmesh is being modified in a strange way, along with a number of PointOnEdgeExceptions.
After some testing, I found out that Capsule/Capsule and Box/Box overlaps work, just not between different shapes.
This definitely looks like a bug to me, but at least it can be resolved by ensuring that no props with different shapes overlap!