I spoke with a Nelnet Rep

The man on the phone who helped me was actually very patient. For my situation, my account has been past due and all of my auto and manual payments wouldn't go through. He mentioned that there has been an update or change to the website, and some background operations may have something to do with these issues and they're not sure yet what it is.

He said that in many cases, the saved auto payment will not go through and may need to be deleted and re-added. Since they don't know what exactly is causing these bugs using a debit card or making manual payments each month may be able to get around this. I have to wait till my current processing payment goes away before looking at my saved banking information and can't cancel. So it's a waiting game to see if this will work for me till maybe early next week. Maybe this will help someone else though! He encouraged me to call back if I needed more troubleshooting and to ask for a supervisor.

He also assured me that even though the account is showing past due, there are no penalties being reported against me.

UPDATE This past Monday, I deleted my saved banking information and made a new payment. My payment was posted and confirmed by Tuesday. This troubleshoot worked for me, I hope it will for some of you too.