In a lot of cases this error is related to QMake just putting all the object files in a flat folder in the build directory, which then causes problems if two source files have the same name, even though they might be in different folders. Such as
SOURCES += foo.cpp
SOURCES += bar.cpp
SOURCES += bla/foo.cpp
SOURCES += bla/bar.cpp
In this case QMake would complain about both foo.o and bar.o.
The solution to this problem is to add
CONFIG += object_parallel_to_source
to the .pro file which will cause the build folder to mirror the folder hierarchy of the source tree. Not sure why this isn't the default.
The problem and solution have been previously pointed out here but not in the context of the warning message discussed in this thread.