If you and your spouse both made non-deductible IRA contributions, you would each have your own Form 8606, as you noted.
Make sure the 1099-Rs were reported correctly for each of you, as well as follow-up questions. You may want to delete your spouse's 1099-R and re-enter it.
Click this link for more info on entering Backdoor Roth Conversions.
Here's more info on Form 8606.
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