Boolean difference messes up geometry all by itself
 

The pictures here represent before and after a boolean difference. All the other holes is made exactly the same way, but the last hole messes up everything.

Anyone got some good idea on how to fix this?

After Polygon > Boolean > Difference

Did you receive an error message?

In the error log?

Is the geometry of the other holes lost or just hidden under a plane?

Just hidden under the plane, but I scrapped the part and are doing it in another program, and will import it later, hopfully it will look better. It's a bit sad that maya doesn't work with booleans in a proper volumetric way, I really like modeling like that. But I just have to composite in something and hope for the best. 8)

You should have tried to insert some faces before booling.