It's about what an organization spent compared to their budget. It sounds like 18F was budgeted $0 since they were expecting to earn back their costs in revenue

It's about what an organization spent compared to their budget. It sounds like 18F was budgeted $0 since they were expecting to earn back their costs in revenue by charging other agencies for their services. Since they did not fully recoup their costs, they "lost money". If you budgeted the military $1 trillion and they spent $1.1 trillion, then they would also have lost money.