Sorry @Retsam, but in this particular case I have to disagree with you.
Not because I think that having these 3 illegal faces here will make much difference in the results, but because Kai has put so much effort into this project (as we both have been seeing), and we can be pretty sure that Kai is not looking for ‘eye candy’ results.
If he wanted ‘eye candy’ results, he would have had them within an hour or so of finishing his geometry 
My experience with obtaining ‘accurate’ results is that you MUST follow ‘best practices’, if for no reason other than being able to ‘rule out’ issues like these illegal faces as a reason that you are not getting expected results (which in this case, includes the question, why are my layers collapsing in some places)…
AND, even with ‘best practices’ adhered to, I would consider myself ‘lucky’ if the results were within 15-20% of any experimental data (if the experimental data would even be available, if it is not available then all the more reason to follow best practices)…
@Kai_himself, if you really want to discover where those collapsed layers disappeared to, have a look here…