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.
Notice: We’re sorry to inform you that we are unable to deliver your pre-ordered version of South Park: The Stick of Truth on March 6th as initially planned. The German and Austrian version of South Park: The Stick of Truth contains an unconstitutional symbol which means that we are unfortunately not able to release the game on the German and Austrian market at this time. This concerns all versions/platforms of the game. There is no need to amend or cancel your pre-order. A new release date of South Park: The Stick of Truth for the German and Austrian market will be announced shortly, and we will ensure that your order is delivered to coincide with this new date.

We are extremely sorry for the additional waiting time, and thank you for your understanding.
Low Violence: Low Violence Version