So I wanted to post this work around for the problem with a negative number. A Turbotax tax expert who I worked with suggested manually typing in the "SUMMARY OF PROCEEDS, GAINS & LOSSES, ADJUSTMENTS AND WITHHOLDING" which is the front page of summary form 8949. Instead of importing the form from TD Ameritrade for all stock and option trades, the summary enter was accurate and correct which will be properly reporting gains and losses on Schedule D. No need to import that part of the consolidated statement with all the transactions.
