I let the Program Manager know that I couldn't access the program page in the online portal to upload my documents and today they fixed the bug in the page for me, so I uploaded the documents (almost a week past the deadline). The Program Manager didn't have any problem with it or reference the deadline. I think you will be fine too. Let me know.
I missed the deadline too and am also freaking out. I couldn't access the Program in the Self-Service Portal (maybe because I missed the deadline?) so I just emailed the documents as attachments to the contact person for the documents at IIE for Spain. I hope everything turns out alright for both of us.
I was just accepted to the MA program in Geography at the Maxwell School at Syracuse University! I'm ecstatic. I will receive full funding through a TAship, a 17.5k/yr stipend, and summer research funding. : )