You need to check three things. First, make sure you entered the taxable amount of the pension distribution in Box 2a of the Retirement Income (Form 1099-R) screen. The amount entered in Box 2a is what will be treated as taxable pension income.
Second, check the Box 7 distribution code on the Retirement Income (Form 1099-R) screen to make sure you chose the correct distribution code. Generally, the code will be a 1 if its an early retirement distribution subject to the 10% penalty, or it will be a 7 if it is a normal retirement distribution.
Third, make sure you didn't tell us to to treat the distribution as a rollover. On the Distribution Rollover screen right after the Retirement Income (Form 1099-R) screen there is a checkbox that if marked, will treat the entire 1099-R distribution as being a rollover and not taxed. There is also an amount box on that screen where you can specify part of the distribution as a rollover. Make sure those aren't used if the 1099-R wasn't a rollover distribution.