The preferred option is to crop the whitespace from the PDF file directly. If for some reason this is not possible, I provide a few options in this answer.
Using the bb option by design does overprinting. If you want the portion outside the specified bounding box to not be printed, you have to set the clip option or equivalently, use the starred form \includegraphics*[<options>]{<basename>}.
Here are some examples, where the \fbox{} is only added to show the specified bounding box area:
\documentclass{article}
\usepackage{mwe}
\fboxsep=0pt
\def\test#1#2{\fbox{\includegraphics#1[scale=0.5,#2]{example-image-a}}\vfill}
\begin{document}
\test{}{}
\test{}{bb=0cm 1cm 5cm 9cm}
\test{}{bb=0cm 1cm 5cm 9cm,clip}
\test{*}{bb=0cm 1cm 5cm 9cm}
\end{document}

In any case, it's not really clear what is overprinting anyway: if you correctly specified bb to include only the printed content, nothing should overprint because according to your comments there was only whitespace outside the supposed specified bb.
For debugging the setting of bb, you can temporarily wrap \includegraphics with \fbox{} to see the area contained by bb as I have shown here. Or, as I said at the beginning: go the easy route and just crop the original PDF file (or a copy of it).
bb=Presumably that is not the same as the natural size of the figure which is why it is overprinting. – David Carlisle Apr 02 '14 at 14:11pdf-croptool to get rid of the extra blank space around the edges. make sure there isn't a page number on the powerpoint output. – barbara beeton Apr 02 '14 at 14:39