Literally same issue. I filed for an extension just in case I couldn't finish my taxes in time but I ended up submitting in time. Unfortunately, I realized after submitting the federal returns that the extension had been rejected and the amount that I put down as payment on the extension form had been marked as credit in my actual federal returns. I also can't start on an amendment (1040-X) even though my federal return has already been approved? I'm guessing I have to wait for the state return to be approved too which seems broken.
