The IRS picks up this kind of entry error because they have their own copies of the forms you receive from different issuers and they compare those to your return. TurboTax has what you enter and nothing more. If you say the form you are looking at is a W-2 by entering the amounts under the W-2 section, the program has no reason at all to question your entry.
When you enter that section, the title of the screen tells you you are starting with your W-2s and each W-2 box is presented to you, labeled exactly as it is on your W-2. If what you are looking at is a 1099-R, none of the boxes would match up to the screens, which alerts most people to the fact that they're attempting to enter the form in the wrong place. The program, of course, cannot see the form you are looking at.
