I find that very odd as brokers have been keeping track of cost basis by lots for decades and it's difficult to comprehend how a broker could make this kind of mistake. You might want to ask about this.
Any chance YOU used that lot in your own records, (e.g., Quicken), for the 2012 sale while the broker used a different lot and you didn't catch the difference?
Again, as a practical matter I'm sure hundreds of thousands of sales have their basis adjusted so the simple fact of adjustment certainly shouldn't raise red flags with the IRS. Most brokers these days, I'd guess, even have lot-by-lot basis information available online so you may want to see how closely your information for you unsold lots lines up with theirs.
