You don't add expenses to make it work. Although an expenses is an expense at the end of the day, the IRS does look to see if the Gross Profit is reasonable. COGS is not an expense to play with.
In Quickbooks you would manually enter the information. Purchases made during the year are recorded as either purchases or if you prefer, straight to inventory. To find out the cost of goods sold, you would make a journal entry crediting inventory and debiting cogs.
You enter it virtually the same way in TT. TT should have the beginning inventory already flowing from last year's tax return. Then you tell them the purchases during the year. Finally, you enter the ending inventory. Then they calculate the COGS (they do the journal entry for you so to speak).
A potential error may be that you entered your QB COGS as the purchase amount. Perhaps you had the ending inventory the same as the beginning inventory or maybe you entered it as Zero.,
First thing I would do is to look at the balance sheet to see if inventory is correct. Then work from there.
