Electrical – Battery as reference voltage

Dzarda's comment is valid. You have about 29uA's of current flowing through there at 12V supply and even less as your battery voltage drops. The Zener voltage will depend on the current flow through it. The lower of a resistance you have supplying current, the easier it will be to keep the Zener voltage relatively constant/stable.

You'll definitely want to look into Dirceu's comment and make sure the output of the comparator is rail to rail and isn't open-collector or open drain. If it is, adding a resistor as he recommended will work.

I think the main reason this will likely work poorly is because there's no hysteresis in it. Depending on the current draw of the circuit, you'll end up with some voltage drop due to the internal battery resistance. As soon as this limiting circuit cuts off the current, the terminal battery voltage will jump back up because no current is flowing. That wall cause the circuit to turn back on, which in turn will cause this limiting circuit to shut it off, endlessly turning on and off the circuit. This may work for your purpose, but the main circuit may get quite confused and you'll generate a lot of noise. If you have a comparator with hysteresis built into it, or if you add hysteresis to this circuit, that will be avoided.

Your current resistors show that you'll cutoff at about 10.11 volts: 9.1*1000k/900k = 10.11 V.

Lastly, although Ignacio is correct that Zener's aren't great voltage references, you don't need anything terribly accurate for your application.

I suspect that you are connecting Aref to the regulator output.

While you have sufficient voltage, and the regulator provides the correct (i.e. expected) voltage, you get correct readings.

When the battery falls below a limit, the output at the regulator falls, and will always be the input V minus its drop. The ADC will always read the same voltage (since regulator output = Aref = Battery - Reg. Drop), which happens to be a higher ADC value than before this condition.

You need a better reference voltage at Aref. You can, for example, use a Zener with a drop less than 2.8V, and a voltage divider to feed the ADC.

Update: (Regarding your comment) You should add a better reference voltage to Aref. Since you observe the problem it is a good practice to fix it. Your arduino the way it works now cannot tell whether the battery is dead or fully charged, which is not a good idea.

Another point is that you risk damaging your arduino, as you are bringing Aref above Vcc. There is limit for this (I can't remember, check datasheet).

Finally is is also a bad practice to rely on something you observed (and it is not a guaranteed specification), since it may soon behave differently. Save yourself from headaches, and design following good practices.