It's been over a year since I had this problem but I think I remember what happened.
I had filed an extension using Turbotax Quick Extension website (I think that's what it is called). The extension was successfully filed. But when I went to file the actual tax return, the software said that the return was already filed. I logged into the IRS website and saw that the extension was there, but no tax return.
For several weeks (and maybe months) I struggled with Turbotax support. Most support staff didn't understand the issue. I think it was eventually escalated which resulted in a software update. After I applied the update, everything worked.
So the issue was actually a backend Turbotax problem where their system (and the software) saw an extension filed but interpreted it as a return.
