It can be the case that the brokerage does not have the correct basis. In that situation it is your responsibility to report the correct basis, explaining why you are correcting it, and be ready to provide the appropriate documentation if the IRS questions it after you file. This is true for many other tax situations as well. Just because someone else reports or is required to report does not mean you are no longer responsible for what you file, whether the difference is in your favor or not :-). At least that's how i understand it. It can't hurt to include an explanatory note in the return any time you are correcting (or disagreeing) with what someone else is reporting. Doing that is the sort of good practice a tax program can't do for you!
