BLDGBLOG shows us some of the "twisty little passages" found underneath several churches and farms in Bavaria, and featured in Der Spiegel. The passages form "very small labyrinths" with "Schlupfe (slips)" that are "only 40 centimeters in diameter". Almost nothing has been found in the passages, so they probably weren't places to hold animals or humans for any length of time.
There are lots of them, they're also found elsewhere in Europe, and there are no records of why or how they were built. Werebadgers? Cave Hobbyists? Underground railroad predecessors? Underwear gnomes? Who knows?