Check your entries on your W2 to make sure that they are marked for the correct spouse, and then double-check the entries in the Missouri program for the same.  It sounds like your husband's income is flowing to the form instead of yours, which would also explain why the taxes withheld are also not being credited.

Thanks for the advice but I did all that already. More than once. I spent a couple hours checking and rechecking the numbers. I also used chat and one of the turbo tax people walked through it with me too. I had the same issue with my KS taxes. TurboTax said we owed KS $7000. I went online and did my KS taxes for free on their website and we are getting a refund of $445

turbo tax even shows that the MO portion of my husband’s income is 0 but somehow we owe over $2000 on his 0 income. 

In this public forum we don't have access to your return information.  If there are calculation issues, you may want to contact Customer Support and get their assistance.  What is the TurboTax phone number?