You most likely chose a different status when you went through your state interview, maybe unintentionally. If you didn't file your return yet, you can revisit your state personal section and correct that. If you already filed, and want to change your status, your the only choice to amend your return. 

Hmm, I deleted it all and redid it. It still shows as married filing jointly on federal and defaults to married filing separate on my state taxes. There seems to be no place to change this. Tried going back to personal information several times but this is not an option in state.

Would you clarify which state return(s) are you working?  That may help us directly to the experience.  

I have selected "Married filing Joinly" on my federal, but my Iowa State return is showing "Married Filing Separately".  I did not change my status at any point of the process.  How do I correct this?  I did not have this issue with past uses of Turbo Tax.

@Taskmaster222 

You probably need to start over at the very beginning of he IA tax return.

The IA tax return offers you the unusual ability to file jointly, MFJ-IA, or MFS-IA with both of you on the same tax file.  This is a bit unusual for a state tax return.   Most states don't do this.

The software may have auto-selected MFS-Iowa for the both of you, but you should be able to go back to the very beginning of the IA Q&A and re-select the way you prefer.