I have iBooks 3.2 on iTunes (and my iPad) and iBooks 1.0.1 on my Mac (OS X 10.9.2) in the Dock. Do you have one iBooks app 1.0.1 for computer and iBooks app 3.2 for iTunes and iOS devices?
It seems as though you are asking if the version numbers for iBooks on OSX and iOS are different for everyone else. The answer is that yes, these two apps which have the same name are actually wholly different apps, one for each operating system, and the version numbers are equally different. The most recent versions (as of the time of answering this mail) are 1.1 for OSX, and 3.2 for iOS.