In response, Apple released a second version of the software update for older devices, allowing users to skip the Apple ID login, while the version can also be used to unbrick handsets via a computer, The Guardian reported.
Users are now complaining that a bug caused by the Universal Links feature is causing apps such as Mail, Safari and Messages to crash, after they have clicked on certain links that force sites to open in apps other than Safari.
New York-based Nicholas Carlson wrote: "Suddenly my iPhone is super buggy. Tapping on links won't work. Mail freezes. iCloud burps. My watch won't sync properly."
Another disgruntled user, Mike Dudas, wrote: "The link thing has been driving me nuts the past few days."
Developers Steve Troughton-Smith and Ben Collier linked the problem to the Booking.com app, which had 2.3MB of Universal Links.
Mr Troughton-Smith, who is based in Ireland, tweeted: "Wow http://booking.com literally put every URL they had into their site association file. 2.3MB download."
The file's sheer size caused iPhones to crash and to drain battery faster than usual. While the Booking.com app has been updated, users are still reporting problems.
Other users are reporting not being able to click on links within other apps.
Some of those affected by the glitch have solved part of the problem by disabling JavaScript in Safari.
To disable JavaScript, go to Settings, Safari and Advanced then disable JavaScript.
The Cupertino-based company unveiled iOS 9.3 alongside the iPhone SE and 9.7-inch iPad Pro at its event last week.
The update focuses on sleeping patterns, security and education.
Users are now complaining that a bug caused by the Universal Links feature is causing apps such as Mail, Safari and Messages to crash, after they have clicked on certain links that force sites to open in apps other than Safari.
- Daily Mail