too late to file an extension. there will be no penalties for late filing since you're getting refunds but provided the IRS/state do not find errors that would result in you owing. also, should you need to amend later and owe, there would be late payment and late filing penalties and interest.
if you e-filed and it was rejected, you should have gotten an e-mail rejection notice. however, depending on how your mailbox is set up it may have ended up in the spam folder.
