Including imagery of the swastika in games or other media in Germany is considered a violation of federal law. That's why games that feature Germans in World War II have to be heavily edited prior to release in that region.

Unfortunately, it seems as though the wrong version was reproduced and sent to Germany that does not include censoring of a few scenes containing the swastika. Whoops!

Here's a translated excerpt from Gameswelt that details the issue.
How us an anonymous source has happened, seems the USK version of South Park: The staff come to be the truth uncut in the trade. Thus, not only the previously discussed contain scenes but also unconstitutional content such as swastika clearly visible in the USK version can be seen.

The full version is anything but planned: So the false "master" version is to come in the pressing plant, and thereby the various misstrike have arisen. At our request Ubisoft declined to comment on the allegations. We will keep you more up to date.

In fact, the game listing on Steam for that region also includes a warning that the game will now see a slight delay while Ubisoft and Obsidian fix the content.