From what I recall, a girl who is about twenty years old finds herself in a strange and gloomy stop-frame animated city. A very distinct scene, which should identify the film, involves the girl being captured by a creature described as follows. It was like the walking skeleton of a long four-legged creature about the size of a bus. Apparently the girl broke some rule and this creature clamped it's ribcage around her and trotted her off to jail.
If I had to guess a year, it would be between 1996 and 2006.