I understand the system is meant to indicate that something has been submitted. I've also worked with similar ropey I.T systems, but there's no excuse really.
I suspect Rovers argument is that by uploading the documents and clicking 'Save', the documents were 'sent' to the League (i.e they were uploaded onto the League's servers before the 11pm deadline) but just weren't accessible in the system's front end to the League. That is something that EFL developers should be able to confirm in the database very easily. However, there's some assumptions there on my part about the technical set up of the system.
After last year, the final step of the process should either be to print a copy / take a screenshot of any confirmation from the system then ring the league and confirm they have received the paperwork.
I like Gregg, but it's a big oversight on his part if that wasn't added to the process. I don't see how his position is tenable after what he said last year and the same for Ian Silvester. They should both walk - I think Gregg does, but Silvester doesn't bother.