1. Have a simple program (project attached):

   #include <QCoreApplication>
   #include <QDebug>
   #include <QDir>
   #include <QFileInfo>
   #include <QLibraryInfo>
   
   int main(int argc, char *argv[])
   {
       QCoreApplication a(argc, argv);
       const QString binPath = QLibraryInfo::location(QLibraryInfo::BinariesPath);
       qDebug() << "binPath:" << binPath;
       QFileInfo fiDebug(QDir(binPath), "Qt5Cored.dll");
       qDebug() << "contains debug binary:" << fiDebug.exists();
       QFileInfo fiRelease(QDir(binPath), "Qt5Core.dll");
       qDebug() << "contains release binary:" << fiRelease.exists();
   
       return 0;
   }
   

2. Build this.
3. Run it:

   D:\Testprojekte\location>debug\location.exe
   binPath: "D:/dev/32/MSVC2015/qt-5.7.1-desktop/qtbase/bin"
   contains debug binary: true
   contains release binary: true
   

   In other words, works as expected.

4. Run windeployqt on the program:

   D:\Testprojekte\location>windeployqt debug\location.exe
   D:\Testprojekte\location\debug\location.exe 32 bit, debug executable
   Direct dependencies: Qt5Core
   All dependencies   : Qt5Core
   To be deployed     : Qt5Core
   Updating Qt5Cored.dll.
   Updating concrt140d.dll.
   Updating msvcp140d.dll.
   Updating vccorlib140d.dll.
   Updating vcruntime140d.dll.
   Patching Qt5Cored.dll...
   Creating D:\Testprojekte\location\debug\translations...
   Creating qt_ca.qm...
   Creating qt_cs.qm...
   Creating qt_de.qm...
   Creating qt_en.qm...
   Creating qt_fi.qm...
   Creating qt_fr.qm...
   Creating qt_he.qm...
   Creating qt_hu.qm...
   Creating qt_it.qm...
   Creating qt_ja.qm...
   Creating qt_ko.qm...
   Creating qt_lv.qm...
   Creating qt_pl.qm...
   Creating qt_ru.qm...
   Creating qt_sk.qm...
   Creating qt_uk.qm...
   

5. Run the program again:

   D:\Testprojekte\location>debug\location.exe
   binPath: "D:/Testprojekte/location/debug/bin"
   contains debug binary: false
   contains release binary: false
   

   This path is obviously wrong. It should not have the "bin" subdirectory.

With Qt 5.4.1 I could not reproduce this.