If the excess was not doubled on Form 8889 line 13, it seems like the excess might not be handled on Form 5329 correctly, perhaps omitted from Form 5329 entirely. As far as I can tell, TurboTax adds the amount from line 2 to the amount from line 43 of Form 5329 and puts the result on Form 8889 line 13.
Doing an override voids the accuracy guarantee.
