I know your question very well, because over the years as an investor myself, I've experienced many fractional sales of shares, in many different ways, through several different brokerage firms. These can happen for reasons of corporate reorganizations, the sale of a position where dividends were being reinvested, etc.
The reporting is not always consistent in the brokerage statements, and TurboTax does indeed ask for some value (both cost basis and sales proceeds) in order to complete Schedule D and Form 8949 (reporting requirements for stock, bond, and mutual fund sales).
Even though TurboTax will accept the input of $0.01 per share in the data field, the program follows the convention of rounding down anything that is 49-cents or lower, and rounding up anything that is 50-cents are higher -- to the nearest whole dollar.
Therefore I find that in situations like these, where the gains and losses are negligible on a fractional share(s), and don't even rise to the level of a whole dollar, a good solution is to input the cost basis and net proceeds both at $1 for the given entry. If you have multiple entries to make, for different securities or because some are "covered" and other "uncovered" the (new) IRS basis reporting rules categories, then you can enter each as separate $1 transactions (effecting no gain or loss).
By doing so, the transactions don't get rounded up, or down, it causes no problems in the software, and the IRS will see that you are reporting something with a positive value (albeit just a dollar). The IRS will not be concerned if your actual gain or loss is less than a dollar, as it will cause absolutely no impact on your income tax refund (or tax liability owed).
I find this to be a very workable, and fair, solution to the issue.
Thank you for asking this question.
