There are a few tax forms and charges included on your annual Form 1040 that actually are separate filings. Form 5329 is a good example; this form is for various penalty excise taxes, not income tax, and it can be filed standalone as well as together with Form 1040.
Amending and requesting refund of these extra taxes similarly cannot be accomplished with Form 1040-X alone, even if TurboTax prepares the form that way.
In the case of penalty taxes like underpayment penalty, the way to request that refund is to include a Form 943 for the Penalty Abatement together with Form 1040-X for the income taxes changes that justify it!
