The Apple documentation on Info.plist keys states that both CFBundleVersion and CFBundleShortVersionString should be version numbers in x.y.z format. qmake currently expands @SHORT_VERSION@ to x.y instead of x.y.z.

As a result, Finder's Get Info only displays the major and minor version components but not the patch level.

Please extend the @SHORT_VERSION@ expansion code in ProjectBuilderMakefileGenerator::writeMakeParts() like this:
plist_in_text = plist_in_text.replace("@SHORT_VERSION@", project->first("VER_MAJ") + "." + project->first("VER_MIN") + "." + project->first("VER_PAT"));

Documentation reference:
https://developer.apple.com/Library/ios/documentation/General/Reference/InfoPlistKeyReference/Articles/CoreFoundationKeys.html#//apple_ref/doc/uid/20001431-102364
https://developer.apple.com/Library/ios/documentation/General/Reference/InfoPlistKeyReference/Articles/CoreFoundationKeys.html#//apple_ref/doc/uid/20001431-111349