qmake, the build tool provided with the Qt toolkit, converts project files written in its own mini-language to platform-specific Makefiles.
This process includes adding necessary dependencies to the Makefile, so that changes in source files trigger rebuilding of the outputs that depend on said sources.
If your project is spread across directories, you'll likely add an INCLUDEPATH line to your .pro file so that the #include directives look sane -- say #include "library/foo.h" instead of #include "../library/foo.h". This can be done by adding INCLUDEPATH += "../" to the .pro project file.
This, by itself, doesn't cause the files in include directories to be treated as dependencies. This is a sane default, since you likely don't want to rebuild your whole project if a system library changes -- assuming, of course, that the library is meant to stay binary compatible between releases!
Thus, if any of your source files references a file from somewhere within INCLUDEPATH, it won't cause a dependency for that file to appear in the Makefile. You have to add the path to DEPENDPATH, too.