I think I found the issue. The "income" displayed for each city (on the map under city name for example) is the net income of the settlement. It is the income minus the corruption. You can check. Look at the details for the settlement. If you add the income from farms, trade, taxes and admin, you will not get the income that is displayed for the city, unless you also subtract the corruption. The fact that the difference between corruption income and corruption expenditure is 58 is not ironic at all, but a consequence of counting corruption twice. I haven't looked at the upkeep discrepancies yet.