It isn't all too uncommon a smaller update is rolled out following major operating system update, addressing bugs and other hiccups that popped up. Following the release of iOS 9.3, the bugfix update to iOS 9.3.1 was sorely required. In the last few days, millions of Apple users were plagued by bust link-handling, opening certain links saw the device crash.
The error not only occurred in certain applications, but also both in native and non-native apps. Safari, Mail, Messages, Notes were all affected, as well as Chrome, Booking and numerous other apps. Apple hasn't provided any details just what exactly it did to root out the bugs and errors. Apparently, however, the universal links and shared web credentials were plagued by the bugs, which are responsible for the exchange of information between the system and the apps.
In today's update to iOS 9.3.1 Apple has also included a few security updates that did not make it to iOS 9.3. As always, the update is available via Software Update and is a small download of just about 20 MB.