I have sent more than a few emails to them about this issue. All the Cocoa Xcode GUI screen shots are omitted in the pdf.
I also have some issues with older Head First pdf looking garbled on the iPad.
Latest releases are not a problem
I have used iBooks, Goodreader, and Readdle with the same result.
There are some fundamental issues to be fixed here. I suspect it has something to do with the screenshot format of the Xcode GUI