Turbotax prepares Form 8960 but does not exclude income from 401(a) pensions

That can happen if you enter a code "D" in box 7 on your Form 1099-R reporting your pension distribution. That would mean it would be treated as an annuity. Can you clarify what entries you have on your Form 1099-R?

Not quite sure what you mean by excluding 401(a) pension income  The taxable amount of 401(a) distributions is excludible from Form 8960 line 3 but is not excludible from line 13.

If you received a 1099-R reporting a distribution from a 401K, this is normally taxable income, as you received a tax break for your contributions.  

Be sure to enter your form exactly as issued.  If this applies, you don't need Form 8960 in your return, unless you have other investment income.  If not, you can delete this form from your return. 

Be sure to clear your Cache and Cookies first if you're using TurboTax Online. 

Here's more info on 401K Plans.

@jsim1