You most likely have a resource that is a parent of itself or two resources that are parents of each other. It can happen when you drag resources around in the tree.
If you delete all files in the core/cache directory, it will delete anything Wayfinder has cached, but it won't solve your problem if the 'parent' fields of any resources are invalid.
If you know the resource you changed, you can edit its 'parent' field in the modx_site_content table in PhpMyAdmin (you can just make it a 0 -- that will put it at the root and you can try again). Be sure to delete the files in the core/cache directory after making the change.
If you don't know which resource it is, SiteCheck might help, it will check the validity of the parent field of all resources:
http://bobsguides.com/sitecheck-promo.html