According to a page on Apple's website, the problem seems to affect users who travel between time zones. For whatever reason, when the time zone switches it prevents the battery indicator from updating properly. The company said that it's working on a fix but didn't specify when users can expect the problem to stop.
If you're having trouble, Apple recommends the following steps:
The bug doesn't appear to affect the actual battery life of the iPhone 6s and 6s Plus, simply the way that it's displayed on users' phones. Apple has taken some flak for the battery life on the latest models, prompting the company to release its own battery case.