Cases of battery percentages on iPhone 6s and 6s Plus not updating, resulting in inaccurate readings, have been reported since September 2015. Now Apple has narrowed down the catalyst for the bug being the time changing -- either manually or when travelling through time zones. While a fix is being worked on, here is a workaround.
Apple is "aware of of this issue and is investigating the cause and a solution."
In the meantime, the following is suggested:
- Restart your iPhone
- Go to Settings > General > Date & Time and make sure that Set Automatically is turned on
- If this happens again and you didn't change the time or time zone on your device, contact Apple Support