Erm.. The "loss" of income is actually not a loss. The game distributes your expenses on settlements based on that settlement's population. It grows larger by the disbanded unit, thus, the "burden" of the expenses (building, training, upkeep, etc.) increases on that city alone. It will not reduce your income. Example: Carthage makes 10000 income a turn.. your overall payment is 50000. Carthage's population is 40% of all your land's populations. So the city has to pay 20000, making the number on the map(and details) -10000. If it population grows more negative number upon the city. While actually it is paying off for you more.

Don't worry, you get more tax income as usual. Forget the numbers. Just look at the overall numbers of your kingdom.

As for the bug, I don't know.