ok, i can replicate.
and i don't see anything you would be doing wrong.
the question is: is there an error at all?
i did a quick test and removed the crop and bleed marks in the pdf export and, oh wonder, then the shape seems to be exported as you expect.
i have to ask the experts, but i suppose that the pdf viewer won't show you the overflowing part when crop marks are defined... or scribus is doing something wrong.
ciao
a.l.e