Latest reports say that Apple has confirmed the Battery charge percentage problem on iPhone 6S. An official document has been released through Apple website to help the iPhone 6S customers who are facing the same problem on their devices. The issue seems to be related to the automatic/manual Time zone update settings in the device.
From apple document :
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.
Apple recommends you do the following steps to fix the bug for now and we expect this issue to be fixed in the upcoming version of iOS 9.3.
- Restart your iPhone.
- Go to Settings >> General >> Date & Time and make sure that Set Automatically is turned on.
Apple advises to contact Apple Support if the problem related to battery percentage on your iPhone 6S isn’t fixed even after following the steps provided in the documentation. Apple says that they are investigating on this problem and soon will provide the update fix.