Yes, the Z output gives you one pulse per revolution.
So you can use the Z output to read the count and determine if the count is correct.
If you encoder has X count per revolution, then each time Z signal occurs, it should be in multiple of this count.
And I guess you could also measure the length of each signal, A and B, to filter out noise, however a hardware filter may be a better solution.
Also most commercial quadrature encoders has the following 6 outputs, A, A Not, B, B Not, Z, and Z Not.
I'm not sure if the "A" and "A Not" signals are just inverted (but otherwise aligned) of the same signal or if they are in fact a separate measurement/signal, but by comparing both signals you should be able to guard against some errors at least.
BTW, this is for position control.
Kim