@ISWF ,  I don't  know what prompted you to call your partner as foreign person.  AS I see from your  port:

(a) your spouse is your partner.  You are a citizen and she is not .  So what is her immigration status ?  Work visa or Green Card ?

(b) you file together MFJ -- implying she chooses to be treated as a US person (  Citizen /  GreenCard / Resident for Tax purposes ) .  Thus for tax purposes at least she is a US person.  I quote below  definition of foreign partner  from IRC section 1446. --->

foreign partner

For purposes of this section, the term “foreign partner” means any partner who is not a United States person.

26 U.S. Code § 1446 - Withholding of tax on foreign partners’ share of effectively connected income ...

Once you have the IRS started on your case -- i.e. note CP 282 -- you have to follow through. Explain to them that there is NO Foreign Partner -- it is your spouse ( including her  immigration status ) whom files with you as a  US Person.   Hopefully  they will allow you to correct the filing and go on from there .  You have to respond to their notice ASAP.

Is there more I can do for you ?   Which country is she from ? I am assuming that she lives with you in the USA --yes ?

pk