If you have 2 separate federal returns, you did not file jointly. If you file jointly, you will only have one return for federal and one for state(if you live in a state with income tax).
Look at the top of your 1040. Does it have the Married filing jointly box checked or does it have the Married Filing Separately box checked?
Did one of you file a joint return and one file a separate return?
If it turns out that you filed separate returns and want to change it to a joint return you can Amend Your Return. The amended return will need to be printed and mailed.
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