How do I avoid double-counting of income from employee stock option exercises, when I received both a W-2 and a 1099-B for the same transaction?I

They are complimentary documents.  The reason why is the W2 is reporting the stock that was included in your income, and the 1099-B reports the sale of the stock (when you cashed it).  This results in two separate taxable events.  Being paid with the stock is included as wages or salary, which is why you received the W-2.  Cashing it out creates a capital gains (or loss) transaction, which is reported to you on Form 1099-B, but you will report with Form 8949 and Schedule D.  Since the two numbers are very similar, your capital transaction will be very small (small gain or small loss). 

TurboTax will guide you through this.  See this FAQ on how to enter the 1099-B on your stock sale:  https://ttlc.intuit.com/replies/3301668