You sometimes find that the battery indicator on the display and the battery itself will differ.
My understanding of this is because the display is showing predicted battery life less based on the usage data the systems has gathered since you turned the bike on (i.e it is analysing the power usage of your ride), whereas that battery indicator is just showing remaining capacity (be aware the lights on the battery don't go off at linear intervals, you will often find you use 2 bars over a long period then suddenly go down to 3 then 2).
Quite often if you turn the bike off, then on again the battery levels will sync up again.
I haven't heard of a 2 bar discrepancy before - sometimes there are software updates to the battery as well, maybe this needs to be done?
Also if a bike is derestricted it can sometimes play tricks with the display info.