This error is not related to Mac OS X 10.9!
Running make package delivers the following error:

/Library/Developer/CommandLineTools/usr/bin/install_name_tool: the LINKEDIT segment does not cover the end of the file (can't be processed) in: /Developer/dartclients/dc_mitk_release_installer/MITK-Superbuild-Release-nightly/MITK-build/_CPack_Packages/Darwin/DragNDrop/MITK-2014.03.99_rc2335c-mac64/ALL_IN_ONE/lib/CppMicroServices/libCppMicroServices.2.99.0.dylib
/Library/Developer/CommandLineTools/usr/bin/strip: the LINKEDIT segment does not cover the end of the file (can't be processed) in: /Developer/dartclients/dc_mitk_release_installer/MITK-Superbuild-Release-nightly/MITK-build/_CPack_Packages/Darwin/DragNDrop/MITK-2014.03.99_rc2335c-mac64/ALL_IN_ONE/lib/CppMicroServices/libCppMicroServices.2.99.0.dylib
globbed plugins:
/Library/Developer/CommandLineTools/usr/bin/install_name_tool: the LINKEDIT segment does not cover the end of the file (can't be processed) in: /Developer/dartclients/dc_mitk_release_installer/MITK-Superbuild-Release-nightly/MITK-build/_CPack_Packages/Darwin/DragNDrop/MITK-2014.03.99_rc2335c-mac64/ALL_IN_ONE/MitkCoreApp.app/Contents/MacOS/libCppMicroServices.2.99.0.dylib
/Library/Developer/CommandLineTools/usr/bin/install_name_tool: the LINKEDIT segment does not cover the end of the file (can't be processed) in: /Developer/dartclients/dc_mitk_release_installer/MITK-Superbuild-Release-nightly/MITK-build/_CPack_Packages/Darwin/DragNDrop/MITK-2014.03.99_rc2335c-mac64/ALL_IN_ONE/MitkCoreApp.app/Contents/MacOS/libMitkCore.dylib
/Library/Developer/CommandLineTools/usr/bin/install_name_tool: the LINKEDIT segment does not cover the end of the file (can't be processed) in: /Developer/dartclients/dc_mitk_release_installer/MITK-Superbuild-Release-nightly/MITK-build/_CPack_Packages/Darwin/DragNDrop/MITK-2014.03.99_rc2335c-mac64/ALL_IN_ONE/MitkCoreApp.app/Contents/MacOS/libMitkDICOMReader.dylib
/Library/Developer/CommandLineTools/usr/bin/install_name_tool: the LINKEDIT segment does not cover the end of the file (can't be processed) in: /Developer/dartclients/dc_mitk_release_installer/MITK-Superbuild-Release-nightly/MITK-build/_CPack_Packages/Darwin/DragNDrop/MITK-2014.03.99_rc2335c-mac64/ALL_IN_ONE/MitkCoreApp.app/Contents/MacOS/libMitkDataTypesExt.dylib
/Library/Developer/CommandLineTools/usr/bin/install_name_tool: the LINKEDIT segment does not cover the end of the file (can't be processed) in: /Developer/dartclients/dc_mitk_release_installer/MITK-Superbuild-Release-nightly/MITK-build/_CPack_Packages/Darwin/DragNDrop/MITK-2014.03.99_rc2335c-mac64/ALL_IN_ONE/MitkCoreApp.app/Contents/MacOS/libMitkFiberTracking.dylib
/Library/Developer/CommandLineTools/usr/bin/install_name_tool: the LINKEDIT segment does not cover the end of the file (can't be processed) in: /Developer/dartclients/dc_mitk_release_installer/MITK-Superbuild-Release-nightly/MITK-build/_CPack_Packages/Darwin/DragNDrop/MITK-2014.03.99_rc2335c-mac64/ALL_IN_ONE/MitkCoreApp.app/Contents/MacOS/libMitkPlanarFigure.dylib
CMake Error at /Developer/dartclients/dc_mitk_release_installer/MITK/CMake/BundleUtilities.cmake:773 (message):

error: verify_app failed

Call Stack (most recent call first):

/Developer/dartclients/dc_mitk_release_installer/MITK/CMake/BundleUtilities.cmake:655 (verify_app)
/Developer/dartclients/dc_mitk_release_installer/MITK-Superbuild-Release-nightly/MITK-build/Modules/DiffusionImaging/MiniApps/cmake_install.cmake:263 (fixup_bundle)
/Developer/dartclients/dc_mitk_release_installer/MITK-Superbuild-Release-nightly/MITK-build/Modules/DiffusionImaging/cmake_install.cmake:37 (include)
/Developer/dartclients/dc_mitk_release_installer/MITK-Superbuild-Release-nightly/MITK-build/Modules/cmake_install.cmake:57 (include)
/Developer/dartclients/dc_mitk_release_installer/MITK-Superbuild-Release-nightly/MITK-build/cmake_install.cmake:95 (include)