s3d does things like that, some of it is preparation for adding stuff in later layers.

For example, If you have text you'll notice it starts the text quite a few layers before it actually surfaces. I think it just adds things like that to make the part stronger below or around certain parts.

And for that particular stl. John cut the centre out of the original effector, resized it and then plugged the original centre back in - which is why it shows the rectangle.

It shouldn't effect the print - I've printed that part a couple times with no issues.

How many top and bottom layers are you using ?