Even without that file, its clear that there are angled faces on the top of the parts of the part you have marked.
The one with the step obviously has a very shallow angle on the top face....and the other two may have small chamfers on the corners...or an even shallower angled top face.
Viewing the shape data from the factory file will reveal what's wrong.
Viewing the screenshots closer.....it may even be an issue in the mesh. Even more sure viewing the shape will answer the question.....