How do I fix flags during federal review of my short put options which lost money?

So whenever I sold short a put option, Etrade entered zero under Box 1e (Cost Basis) and put the total net gain or loss in Box 1d (Proceeds).  The same number is then reflected under Gain/Loss amount.  I doubled checked that the numbers entered into turbotax are exactly how Etrade entered it on my 1099-B.  On all short puts that were a loss, Etrade is flagging them.  The total numbers add up as well.  Do I just ignore the flags and click through them in turbotax?  How should I handle this?