It's a bit difficult to figure out exactly what happened since you provided rounded numbers in your original question, but removing the entry for your own personal contribution largely or completely removed the excess contribution. When you removed your wife's personal contribution that she did not make, that removed the corresponding deduction, increasing AGI and taxable income. It's likely that the increase in AGI also caused a side effect, perhaps something like a reduction in earned income credit or a reduction in a Retirement Savings Contributions Credit. Compare your Form 1040 and Schedules 1 through 3 with and without the change to your wife's personal contribution to see what side-effects might be at play.
The large increase in tax liability when removing your wife's personal-contribution entry seems to suggest that you might benefit greatly from increasing your HSA contribution to the maximum $7,000 combined by actually making personal contributions to one or both HSAs by the July 15, 2020 contribution deadline.
