Hi Stefan,

> I'd like to ask how one does debug this kind of problem? Where do you begin and what are you looking for?

So like the others mention above the thing you want to look for are "Naked edges" - those are edges that belong to only one surface instead of being joined between 2 surfaces.

Areas that have naked edges break the "water-tightness" of the object's skin and those are the spots that will need to be repaired in order to make the object a full solid.

In order to see the naked edges you have to set up a shortcut key with a script on it as described here:
http://moi3d.com/forum/index.php?webtag=MOI&msg=6051.2

Once you set that up, push the N key to get the naked edges highlighted and then you can zoom in to those areas to closely inspect the model there.

Please let me know if you are still stuck!

- Michael