After you completed entry of the Form 1099-R one of the following screens asked you what you did with the money. You should have selected that you rolled the money over to another account or the same account and entered the amount rolled over.
On your Form 1040 if the distribution was from an IRA the taxable amount, if any, will be on Line 4b. If the distribution was from another type of tax deferred account, the taxable amount, if any, will be on Line 5b.
Look at your Form 1040. Is the taxable amount entered on either 4b or 5b correct?