Apple released a minor update to their iBooks app for iOS yesterday, The update is the first maintenance update in 6 months for the app, brings the version up to 3.1.1, and is meant to fix compatibility bugs with iCloud.
From the release notes:
What’s New in Version 3.1.1
This version of iBooks improves compatibility with iOS and iCloud.
While it’s not clear exactly what bugs have been fixed, or aspects of the app have been improved, it’s thought to be related to complaints on the Apple Support Forums regarding improper bookmark and page render syncing between devices. It also likely includes optimizations to ensure compatibility with iBooks for Mac, due for release alongside OS X Mavericks this fall.
iBooks is available now as a free download from the App Store.