After setting GOBJECT_DEBUG=objects comparing the outputs
of the following program run with ITERATIONS set to 2 and 1:

#include <gtk/gtk.h>

#ifndef ITERATIONS
#define ITERATIONS 1
#endif

int
main (int   argc,
      char *argv[])
{
  if (gtk_init_check (&argc, &argv))
    {
      int i;
      for (i = 0; i < ITERATIONS; ++i)
        {
          GtkWidget *dialog;
          dialog = gtk_file_chooser_dialog_new ("Open File",
                                                NULL,
                                                GTK_FILE_CHOOSER_ACTION_OPEN,
                                                "Cancel", GTK_RESPONSE_CANCEL,
                                                NULL);
          gtk_widget_show_all (dialog);
          gtk_widget_destroy (dialog);
        }
    }

  return 0;
}

on Wayland the number of objects alive at exit increases for the 
presence of few GdkFrameClockIdle objects.

The problem is that on Wayland popover GdkWindow have window_type
GDK_WINDOW_SUBSURFACE

https://git.gnome.org/browse/gtk+/tree/gtk/gtkwindow.c?h=gtk-3-22#n6647

and gdk_window_destroy (_gdk_window_destroy_hierarchy) does nearly nothing
for this kind of GdkWindow:

https://git.gnome.org/browse/gtk+/tree/gdk/gdkwindow.c?h=gtk-3-22#n2019

in particular it does not unref GdkFrameClockIdle objects it
creates.