Thanks for your quick reply. So I checked the project.pbxproj file and I found the tag explicitFileType = wrapper.application.
To test what will happans, I changed wrapper.application to compiled.mach-o.executable. And a new error was raised:
-- Parse Done --
*** ERROR no C/C++ files found
** Parse failed **
As my project is coded in Objective-C (it is an iPhone project). Does pbtomake support Objective-C ?