On several occasions click-through (dialogs) is just annoying.
Example One: When getting the reward dialog in a mini-dungeon where you have to select one item and the press ok, the character moves with every click.
Example Two: When you are assigning skill points and click 'Confirm' and at the same time another node is beneath that side dialog, you get the error message, that you don't have enough skill points.

Those are not game breaking, just really, really annoying issues that exist since a long time now.