Those with the big numbers in the middle are the newer ones, which replaced the earlier versions in the white frame.
It is the obligation of the publisher to apply these stickers to the boxes/cases according to the audit result of the USK if they aren't already part of the artwork, so they are in no case applied by the stores if that answers your question.
The variations can probably be explained by the fact, that this particular game has been released in the transition phase from the old logo to the new logo (and in between a resize of the old logo was also introduced) and the different new logos are a result of a new system, that had yet some kinks here and there.