The situation:

  mylib/       # This dir should be irrelevant, but isn't!

    mylib.cpp  # This file is added to the build!

  myapp/

    myapp.pro

    mylib/

      mylib.pri

      mylib.cpp

      bar.cpp

    build/     # Doing my builds in here

From myapp.pro, I'm including mylib.pri:

  include(mylib/mylib.pri)

From mylib.pri, I'm adding mylib's sources to the build:

  SOURCES += $$PWD/mylib.cpp $$PWD/bar.cpp

Then I'm running qmake, inside myapp/build:

  rm -rf build && mkdir build && (cd build && qmake ..)

Inspecting the generated Makefile reveals:

  SOURCES = ../../mylib/mylib.cpp
            ../mylib/bar.cpp
            ../myapp.cpp

That's one ../ too many for mylib.cpp! But bar.cpp, which exists only in myapp/mylib/ but not in the top-level copy of mylib/, is resolved correctly.

Clues:

• message($$SOURCES) shows the correct absolute paths, so somehow these are turned into incorrect relative paths at some later stage.
• If I just put the SOURCES of mylib directly into myapp.pro rather than using include(), the problem goes away.
• If I rename the top-level mylib to something else, the problem goes away.
• If I put the build/ directory as a sibling to myapp/, the problem goes away.
• If I put the build/ directory as a sub-sub-directory like myapp/build/build, the problem goes away.