Ok, I just posted pictures and explanations, but apparently I have to post it all again, because it’s not here… One more time:
Here are some randomly generated rooms and ramps floating in the air. You can see that the NavMesh looks just fine:
These are some visualized origin-locations (yellow) on isolated roofs and corresponding “random reachable” destinations (cyan) that the NavSystem gave out for them, connected by a green line:
And here you can see the nonsense results for origins on one particular roof (which isn’t really different from the others):
The same thing is happening for many other areas as well. So what the hell is going on there?? It looks like the origin is off and therefore the destinations are from another “area”, but as you can see, that’s rather unlikely.
The different colors/ambience are just a result of a very fast day-night-cycle, by the way.