Everyone's experienced this problem.
Kobo has implemented fixes to gauge better battery life in the indicator and to give you a low battery warning in the newer firmware versions (have yet to see the warning actually work myself).
If your Kobo is new it'll happen more frequently as the battery hasn't been cycled/calibrated with the hardware/software to have a really accurate reading. After a few full discharge and recharge cycles it gets better.
I only charge my Kobo when it shuts down on me like that and each time the battery indicator gets better.
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