P&L STATEMENT

If your expense item has a negative sign, decreasing the invoice, then this is how QB will behave for some item types (parts, inventory, other charges, and service types at least), because the negative line item is treated as a return, presumably of some thing you previously sold, and then is 'applied to' the other invoice lines like a Payment is applied. The return, 'applied' to the invoice is considered the end point of the sales process, and so is recognized as a cash basis event. You'd get the same result if you created a Credit Memo using that item and the applied it to the invoice, decreasing the invoice balance.

You can avoid this behavior by using a Discount type item for the expense item, which behaves differently and is assumed to be part of the sale, not a return of something.

Discount item will show as partial expense on the income statement and not the full expense deducted from the invoice. 

Discount item is still increasing the income too in the P&L. 

Even when I delete the item line and I try journal entry (Debit Expense, Credit A/R), and I link the journal entry to the open invoice, the income is still increasing in the P&L.