transferring over 12500 without filling in that harmless statistical form, is a misdemeanor, this story doesn't make sense

and btc transfers do certainly not fall under the limit, this is only a central bank statistical tool...
unless they were using the misdemeanor charge for a search warrant, which would not be a suprise, in Germany a search warrant can be obtained for almost no reason at all. Trouble is that many countries, Germany included, evidence found via illegally obtained search warrants, CAN be used in court, so it is a very popular tool
In US that evidence would be worthless

Bitcoin will always attract both users and authorities who will look for opportunities to punish the Bitcoin user. And note that this is only in countries where Bitcoin is not legal.