Indeed but this penalty is calculated at day change and then will affect your output for the coming day.
You must have a negative money output at day change for not beeing able to pay your spies. And still, it will not affect your spies payment as we are talking about a "T-Time" which is day change. In our concrete case we are talking about, the player had the required money to pay his spies at day change, no money is removed from his stockpile from upkeep at the exact time of calculation. It can't explain the loss of spies.
You must have a negative money output at day change for not beeing able to pay your spies. And still, it will not affect your spies payment as we are talking about a "T-Time" which is day change. In our concrete case we are talking about, the player had the required money to pay his spies at day change, no money is removed from his stockpile from upkeep at the exact time of calculation. It can't explain the loss of spies.