If you are looking at a summary screen or review screen those show the full amount as income and lump a lot of stuff together. You need to check the actual 1040 form and make sure it's right. It should be on line 5a and 0 taxable on 5b with the word Rollover by it.
After you entered the 1099R did you answer all the followup questions? Oh, what code is in box 7?
Pick I moved it to another retirement account even if you put it back into the same account.
Then choose - I did a combination of rolling over, converting or cashing out the money