There ia a difference between having to include an army of millions that personified battles of WW2 because you'd lose all historical relevance without it, and including badges of a small unit, especially one you could substitute with another that played similar role but wasn't known to comprise of Nazi followers or commit murders of civilian population.
In their own game (as opposed to modifiers introduced by posters) Relic stay away from the obvious snares (as turbotortoise stated), not least bcs they do not want to run foul of Germany's legislation, where part of their market lies. If Relic have introduced a design concept which links to any WWII unit which had a dubious reputation, it will almost certainly be by accident.
e,g, look at the lengths to which Relic went to disguise the SS as Knights Cross Holders in COH1. You see neither runes, nor swastikas.
The unpleasant truth for those of Allied heritage is that as we draw further away from 1945, the effects of Allied propaganda become more clear. "To the victor, the spoils".
e.g You wrote a thread very recently about the UK Commandos: they were created as hard-edged units which might strike as much fear, as their German equivalents in the SS did. It was not an accident that the Commandos were originally designated Special Service troops (abbreviate!), nor that their first brigade was the SS Brigade, until it was eventually retitled in late 1944. Commandos were designed to strike fear into defending troops on the Axis borders, and they did. Hence 'the Hitler order', which stated all Commandos captured were to be executed.
If you read '18 Platoon' by Sydney Jary, you can see how an ordinary UK infantry unit was given orders in advance to shoot any German PoWs on sight, if a situation went bad during the approach to Arnhem.
And there are many instances of this kind of thing. Maybe not casual, deliberate wholesale slaughter, in the way that some SS Units like Das Reich behaved at places like Oradour-sur-Glane, but 'war crimes' nevertheless on a lower scale.
If you play any game like the COH franchise, you have to pinch yourself and remember that gameplay>real life. You have to suspend moral judgments, since it is a videogame. If you feel morally uncomfortable, you should not play the game.
But of one thing I am clear: this game was not created for you to make those moral judgments. it is as far away from reality as you can hope: Russians fighting in France? USF or UKF fighting in the Soviet farmlands? Shermans and Cromwells taking down Tigers easily? Extensive deployment of the Landmattress? No! no! no!