When I printed my1040, the last box was checked under Filing Status for a non-resident alien spouse, even though I did not say she was alien. How can I correct this?

You must have inadvertently check the box in the My Info  section.  To correct it it in TurboTax Online, open your return and from Tax Home click on Personal Info and then Continue.  Under "Your household" click on the down arrow next to your wife's name, then click on Revisit.  Continue through the screens until you get to "Tell us a bit more about [Wife's Name].  Towards the bottom of the list is a check box for [Wife] is a nonresident alien or dual-status alien spouse.  Be sure to that box is not checked, then click on Continue.