I don't know Nico, I don't use subcategories.
I wasn't suggesting that the widgets are the problem, I wanted you to check them first.
If you reset all the widgets to the default (ie remove everything from the right hand side) what happens? Do the categories still look wrong?
What about trying (just try, don't have to keep it) removing the parents subcategories and see what happens.
I agree that this is probably a problem with the theme, but if we can provide as much information as we can then it will enable the developers to fix the problem quicker.
Also bear in mind that the theme wasn't necessarily designed by the wp.com team and it will take them some time to fix it.