“Apple is aware of this issue and is investigating the cause and a solution,” although according to Apple, this seems to affect users who change the time on their phones manually, such as when travelling. “If you change the time on your iPhone 6s or iPhone 6s Plus manually or change time zones when traveling, you might notice that the battery percentage doesn’t update.”
The upside here is that Apple has a workaround for you to get the bug to disappear. First you will have to restart your iPhone. Once you’ve done that, go to Settings > General > Date & Time, and enable “Set Automatically”. Once that is done, your battery percentage should return back to your screen.
Unfortunately for users, it seems that this problem was first made public way back in September of 2015, meaning that it has been almost half a year that Apple has not fixed the issue. There have been several iOS releases since then, none of which seemed to address the problem, but hopefully with iOS 9.3, we’ll be able to look forward to a fix. In the meantime if you are affected by this, then try the workaround.