I took a distribution from an after tax IRA, so I only owe tax on the gains, but the financial institution didn't adjust for that on the 1099-R. How do I handle this?

If it is a traditional IRA, you will need to enter the nondeductible contributions (it is a follow-up question to your 1099-R entry).  If it was a Roth IRA, there are a few questions to categorize it as a qualified distribution and nontaxable (once again, go through all of the questions after the 1099-R entry carefully).

Your after tax IRA basis is recorded on the Form 8606 you filed with IRS.

Without it, your distributions are all taxable income.

@barbara-stefl