Can air conditioning cause urine smell?
First, human sweat contains urea, so it doesn't require incontinent commuters. Despite constant cleaning, this effluvia accumulates in the rail cars.
Second, air conditioners precipitate water, entrained dust and volatile organic compounds, making an ideal environment for bacteria, fungi and protists to swim around, excreting their wastes. Microbial volatile organic compounds are none too pleasant, and may have the smell of urine or ammonia (though the waste products of yeast in baking bread can be quite appealing).
Third, there are probably birds in and around the train stations. Birds produce uric acid, which is rapidly converted to ammonia by fecal flora.
Fourth, in older drainage systems, rain water and waste water may be mixed. Given a high water level, wastes may be closer to the surface... or overflow.