I faced with issue during Magento updating from Magento EE to EE 1.13.x. After running script php -f shell/url_migration_to_1_13.php all of my product URL's were changed from <product-url> to <product-url>-1. And weird rewrite rules were added for old URL (check the following image) enter image description here

  • Has Magento answered you yet? There was a URL rewrite bug and a patch for it. (From 1.12) – brentwpeterson Oct 15 '15 at 13:34