Those lines are expected even with a clean only of the application.
There are components of Device OS that are linked into the user application. In particular, the global variables that are accessible to user firmware need to be compiled and linked to the application binary, not the Device OS binary.
Also the make process needs to make sure the static library that contains the stubs to be able to dynamically link with the rest of Device OS (libplatform.a) is up-to-date.