The result was nodes that displayed as set to private in the admincp while actually being accessible by anyone. Setting a node to or from private fixes this by rebuilding permissions properly.
This might affect other areas as well, seems to be that one of the previous pages' actions completed after the more recent actions. Easy enough to just wait for pages to finish loading, but might be an issue with multiple admins working at the same time.
Server Error Mysqli statement execute error : Duplicate entry '0-0-node-47-general-viewNode' for key 'user_group_id_unique' Zend_Db_Statement_Mysqli->_execute() in Zend/Db/Statement.php at line 297 Zend_Db_Statement->execute() in Zend/Db/Adapter/Abstract.php at line 479 Zend_Db_Adapter_Abstract->query() in Zend/Db/Adapter/Abstract.php at line 574 Zend_Db_Adapter_Abstract->insert() in XenForo/DataWriter.php at line 1591 XenForo_DataWriter->_insert() in XenForo/DataWriter.php at line 1580 XenForo_DataWriter->_save() in XenForo/DataWriter.php at line 1381 XenForo_DataWriter->save() in XenForo/Model/Permission.php at line 1140 XenForo_Model_Permission->_updatePermissionsForUserCollection() in XenForo/Model/Permission.php at line 1061 XenForo_Model_Permission->updateContentPermissionsForUserCollection() in XenForo/ControllerAdmin/Permission/Node.php at line 257 XenForo_ControllerAdmin_Permission_Node->_setPermissionRevokeStatus() in XenForo/ControllerAdmin/Permission/Node.php at line 76 XenForo_ControllerAdmin_Permission_Node->actionNodeWideRevoke() in XenForo/FrontController.php at line 310 XenForo_FrontController->dispatch() in XenForo/FrontController.php at line 132 XenForo_FrontController->run() in /var/www/[...]/admin.php at line 13