As far as German forces in North Africa are concerned, there isn't record I could find of any serious war crimes they commited there. Erwin Rommel, the Commander of German forces in North Africa for most of their existance, was well respected by his own forces and his enemies alike and was not known of commiting war crimes nor could I find any record of his troops doing so.

But there were bound to be sub-Saharan Africans there too right?

Not particulary, this page on the historic peoples of Libya says there were small populations of Tebo (Tibbus) people (around 5000) who were of sub-Saharan descent present in Libya before the 1840's before their expulsion, but during the period of WWII, most of North Africa's population would have been of Arab or Berber descent following the Italian Pacification of Libya.