If the tab focus changes during a 'Save As' operation, Geany saves the contents of the tab that obtained the focus in the background while the dialog was open rather than the tab that had the focus when the 'Save As' dialog was opened.
I discovered this when I had a 'Save As' dialog open in what I'll call "Tab A", and then another file associated with Geany got opened, which then opened in "Tab B". Geany now still had the 'Save As' dialog open, but in the background, the tab focus had changed to "Tab B". When I completed the 'Save As' dialog, it saved the contents of "Tab B" to the filename given, rather than the expected contents of "Tab A".
geany 1.22 (built on Jun 20 2012 with GTK 2.24.10, GLib 2.32.3)