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@Kehburton wrote:

As it seems as though the refund is based off of w2 of spouse.

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Not sure what you mean by that.  Each additional $ the couple earns would theoretically change the effective tax rate and possible put them in a higher tax bracket.

Assuming no tax was withheld on the 1099-MISC, as would normally be the case, that there was no overpayment applied from 2018, no ES-tax was paid, and taxes were only withheld on the W-2, any refund would definitely have come from the spouse's W-2's FIT (likely as a result of the W-4 having been adjusted to account for dual earner income).