I'm comparing the situation between Debian stable and Debian unstable.
In both cases, XFCE is used, with xfce-panel and a tray area in the
panel, plus VLC as an example. VLC must be running, so it has an icon
sitting in the xfce-panel tray area.

On Debian stable, right-clicking on the VLC icon from tray pops VLC's
context menu, as expected.

On Debian unstable though, right-clicking on the VLC icon from tray pops
xfce-panel's context menu (more specifically, the one from the tray
applet), which is incorrect. Still on unstable, right-clicking on
Pidgin's tray icon pops Pidgin's context menu, not xfce-panel's, which
is correct.
In fact, right-clicking on any Qt app's tray icon will show xfce-panel's
context menu on unstable.
This might be a regression in Qt or in xfce's systray. I'm unsure.