Here is what I would do to try to drill this down:
1. Make a
backup of your world (call it Test2 or something, but just keep it safe).
2. One by one, eliminate each layer, rebuild routing, check data. So, for example, delete "Objects" layer, rebuild routing, then check routing data. If the problem disappears, then you know that there were objects in this layer that is causing the issue.
3. If the problem is still there, then delete your other layers and do the same thing (rebuild routing, check data).
It's about using the process of elimination to find and get rid of troublesome objects. Remember, you'll be doing all this to your world with a
backup in place, so you can take your experiment and use it for the "good" copy of your WIP.