Okay, a little more explanation:
The Pebble's battery is rated at 3,7V and 130mAh as you can see here
Comparing it to the Nexus 4's battery which is rated at 3.8V and 2100mAh the difference in the capacity holding capabilities is huge.
Note that I said it is their rated
Amperhour values. Since every battery (and everything inside your devices) has its own, unique manufacturing errors, the batteries in the actual devices are close to these rated values.
Let's say my N4's battery can hold in reality 2090mAh, which is 99.5% of the rated value, so it can be easily considered as 100%.
Now if the Pebble's battery hold 120mAh, it is only 92% of the rated value.
So the point is, every app (even the OS) is checking if the battery is full, it is checking the capacity it holds, compares it to the rated value and checks if it is inside a tolerance interval.
Since the Pebble's battery is so small (in every aspect) this tolerance interval has to be very-very small and if your device's battery's actual full capacity is barely outside this interval, the app will not report 100%.
(I hope you got the point, sorry if something is not perfectly clear, English is not my first language)