Current implementation of library dependencies detection works only if dependent libraries are included via header files.
If a .cpp file includes a library, that library won't be detected. An example case is SD library version 1.0.5. See https://github.com/arduino-libraries/SD/blob/1.0.5/src/utility/Sd2Card.cpp#L26

A better implementation, suggested in arduino/Arduino#2792, run gcc -M against every single library file, not just headers