Well, in Witcher it is like that mainly because Sapkowski wrote his books that way. But some elves are also terrorists and brutal murderers in Witcher. I really liked his books because of that, being fed up with the high fantasy stereotype of elves as some kind of übermenschen .
Also, jews were not exactly liked by the general christian population and there were occassional pogroms but most of the time it was not that extreme.
If there is a visit to Prague in Act II or Act III, they might just add a visit to the jewish town. Jews had their own law embedded in the law of the land, their own courts and basically semi-autonomy (the local christian and muslim rulers in Europe and middle east found out it is easier to rule over jews that way as they got the reveneue from taxes anyway and fewer disturbances) so jewish town would be quite a change.
I can imagine some jewish organizations having a problem with a character participating in a pogrom or something like that. Otherwise I don’t see how having would offend anyone (except for nazis ) and raise any controversies that could stifle sales.