It is bad practice to connect batteries in series when they don't have the same capacity. The battery with the smaller capacity will be empty before the larger one, resulting in a lower voltage for the smaller battery. At that point things will start to get interesting as the larger battery will start to charge the smaller one through the connected circuit and with reversed voltage. The cell is not designed for being reversed and charged and bad things may happen a.o.: leaking acid and exploding. Neither of these situations are desirable.
