I noticed this issue on Xubuntu as well as Ubuntu Mate. Apps like Dropbox and HotShots would show a missing icon in the indicator (as in the image). The problem seems to be with Qt based applications and affects Ubuntu 14.10, 15.04, 15.10 and 16.04. Noticed the same problem on Voyager Linux 16.04 too. Here are some temporary solutions that work till the problem gets fixed.
Either start dropbox manually using:
$ dropbox stop && dbus-launch dropbox start
or change the following line in /usr/share/applications/dropbox.desktop:
Exec=dropbox start -i // to Exec=env DBUS_SESSION_BUS_ADDRESS="" dropbox start -i
For HotShots the icon is also missing from xfdashboard. Modify the following lines in /usr/share/applications/hotshots.desktop:
Exec=/usr/local/bin/hotshots Icon=/usr/local/share/pixmaps/hotshots.png // to Exec=dbus-launch /usr/bin/hotshots Icon=/usr/share/pixmaps/hotshots.png