I can't reproduce on by Debian 9, but I didn't yet check with the additional info of QtCreator running.
However, this kind of issue, and especially if QtCreator has to be running, is highly likely to be in either GTK, QtCreator (or Qt), or even X11 (I doubt that last one, but who knows). The save dialog is almost 100% GTK itself, so it's unlikely to be specific to Geany. Could you try with another GTK save dialog, for example GEdit's?