timid bump here, might have a similar (and peculiar) issue :
- Projucer project on Mac where I set the "Application Icon " i.e. Icon(small) and Icon(large) on the Xcode Exporter
- CLion Exporter taking input from xcode+linux+xcodeblocks
When the application Icon is set CLion is actually trying to run the Icon.icns file instead of the executable inside the .app 
if I chmod+x the icon it actually runs it!
Error is
Error running ‘APP’: Cannot run program “/cmake-build-debug/myproject/Builds/CLion/myproject.app/Contents/Resources/Icon.icns” (in directory “/cmake-build-debug/myproject/Builds/CLion/myproject.app/Contents/Resources”): error=13, Permission denied
CmakeLists changes when I add the App Icon is this line, along with all the HEADER_ONLY image lines:
set_source_files_properties (“…/MacOSX/Icon.icns” PROPERTIES MACOSX_PACKAGE_LOCATION “Resources”)