Depends on how you set up the collision on your agents and so on. If you’re using Character controllers for example, you’ll have to make sure their step height isn’t too tall, compared to other agents their height.
At the moment this the package does not automatically clean up graphs.
However I’m working on a third party tool for automatically find connections between graphs, and this will be able to remove unreachable areas. You can read more about it here: Automatic nodelink placer tool - #2 by ToastyStoemp