I already beat Kaos but sometimes I still get money for beating enemies in Story mode. But it doesn't seem to be consistent. Does this happen to anyone else and/or can you explain when you can still get money?
You get more money if you finish the level with more stars (i.e. alive skylanders) than what you have managed in the past. So if you finish it with three skylanders alive, and previously you had only finished it with two skylanders alive, you get more money. The amounts you get paid are shown on the level selection screen.