I received a pension distribution that was rolled over to an IRA but Tubrbotax is still including it as income that should be taxed. How do I fix this?

You should go back to your Form 1099-R entry, edit it without making any changes, and go through the follow-up questions again.

After you have entered the information reported on your Form 1099-R, the follow-up questions are the key to reporting it as a rollover that should have no tax implications.  

One of the first questions you see asks if the money was rolled over to a Roth 401(k) or 403(b) account.  If if was not put into a Roth account, you should select 'no' for this question.  Selecting 'yes' will make the distribution taxable to the extent that there were pre-tax funds in the account.

Then, the next question asks if it was rolled into a Roth IRA.  Again, you should answer 'no' if the money was rolled into a Traditional IRA account.  This 'no' answer is assuming that the pension money that was rolled over simply went to a Traditional IRA or similar type of account.  There should be a message on the screen that explains this and even mentions that if it was rolled to a Traditional IRA you would answer 'no' even though it does not explicitly ask that question.