How do you handle sold Business Asset "profit" when filing taxes?

I sold several business assets last year, and due to depreciation in previous years, made a small "profit" on the sale that is being reported and taxed on Form 4797

 

Here is the clincher, in Quickbooks Self-Employed, the sale is essentially listed as income, so I am already paying taxes on it. (I have them listed as a positive "expense" so you could say they are reducing my expenses rather than raising my income).

 

How do I avoid paying taxes twice?