While Extrusions are supposedly very basic operations I have had innumerable problems controlling them.
The most annoying one involves having an extrusion with a non-uniform cross section.
It is somewhat difficult to explain, but I will try.
Imagine trying to model a picture frame using an extrusion.
First you draw the path (overall size/hape of the frame) and then you draw the cross-section of the frame. The problem appears when the cross-section begins to "stretch" so that when the two ends of the extrusion meet, they are of different sizes.
This problem appears about %70 of the time, meaning sometimes it does, others, it does not.
I assume it is a setting somewhere.