You are confusing some basic reporting issues.
You need to report Short term transactions separate from Long term transactions, which 1099-B is supposed to segregate for you.
What the 1099-B shows at "net" items is not what's important.
What's important is to show the items not only Short-Term vs Long Term, but show Gross Proceeds (Sales Price) vs Cost Basis to determine gain or loss of EACH ITEM. It's apparent that you're looking to report only net proceeds.
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