As a retiree in Pennsylvania my pension is not taxed. Just getting started and I entered my 1099R it says I am getting a federal refund but that I owe the State?

You are correct,  PA excludes retirement income from the definition of taxable compensation. Perhaps you have other income that is taxable in PA, like interest and dividends, and PA tax was not withheld. 

For a list of items that PA includes and excludes from gross compensation, please go to the PA Department of Revenue website by clicking here:  Gross Compensation 

In past years, the PA tax return refund meter would show it's taxed right after you enter the 1099-R in the Federal section......but that was just until you get to the PA interview section, where you would make a selection as to what type of retirement distribution it represented.   

(I Don't have PA set up this year, so I'm not sure they haven't changed that Q&A flow behavior or not for 2020)