There is a way to make an adjustment on the Pennsylvania return to include this contribution in the PA taxable income.
As you go through your PA return, you come to a screen titled "Any other miscellaneous compensation" - click Yes.
On the next screen, you click your wife's name and under payer name, put "HSA Adjustment". For the Type of Income, select "Other income not listed above".
On the next screen, you'll leave the Federal amount blank and enter the PA amount as $406. for Income Description, you can enter "HSA Contribution not made in PA".
These actions will add this back as compensation for your wife on your PA return and it will later be deducted on the PA return, so that the net effect will be a zero HSA contribution made while in PA. The HSA adjustment will get reported on PA-40 Gross Compensation Worksheet as an addition to income
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