Are you talking about cemetaries from the Allied laid out for German KIAs or about cemetaries from Germans for Allied KIAs?

Because in Germany, black or brownish crosses/headstones are completly normal, both for civilian and military graves. Most people used dressed stone, which is also reflected in numerous war cemetaries.

So if we are talking about cemetaries laid out by the Germans, I would go with ignorance (Hanlon's razer etc). If we're talking about Allied cemetaries I'd say it is the opposite, being a sign of respect for the German troops that they get the graves they would get at home.

/e Now that I think of it : There is a German made cemetary for the Canadian soldiers who got killed at Dieppe (Operation Jubilee) : It uses white headstones, like regular commonwealth graves, but they are back-to-back which is typical for German cemetaries, not commonwealth/Allied ones. So I can't really see disrespect, but only ignorane : When digging the graves, they apparently just didn't know how a "normal" commonwealth war grave would look like.