Import .xcodeproj Groups

I am importing an Xcode project into OmniGraffle and it looks like it is trying to organize things based on the Groups in the project. However some of the classes are showing up outside any of the groups and some groups are missing.

Is my project too big?

Am I doing something wrong?

Is there an issue with Xcode version?

It looks like I can manually reorganize the objects into groups, I thought I would check to see if there was an easier solution.

Peter Oppenheimer