Oh dear. The exact reasons why the application were late are not stated in this article but I think two of the comments have it spot-on: 

This is why my institution requires all electronically-submitted federal grants to be completed 7 business days prior to the federally-posted deadline. Screw-ups always happen at the last minute. — Jason Rasgon, Nov 2, 03:16 PM

There is so much information out there that warns submitters about the inherent problems with Grants.gov. Applicants should know better than to wait until the last minute. I would be outraged if federal agencies made exceptions to the deadlines! — Lynn Rollins, Nov 2, 03:43 PM