Let's get them sorted out, WIP2013.
Possible reasons why invoices show as an income on the profit and loss report is that the item you used upon creating the invoice was associated with an income account.
Usually, this happens when you run a P&L report, this will show as income if the period date selected includes the date range for the deposit date, invoice date, and the date wherein the payment was linked.
I'll add this video as your reference as your guide to learn more about Profit and Loss: Understanding Profit & Loss Statement: Income, Cost of Goods.
Let me also share these additional articles to share additional details on what you can do when running reports:
Should you need any assistance getting your income shown on the report, I'm available here to help any time!