I just upgraded an RPi configured as a wireless router to from 15.10 to 16.04. dnsmasq is failing during startup with an unknown interface br0. Before the upgrade, the log showed a wait for auto interfaces to complete, which is missing in the new boot log. When startup is complete, I can log in and manually start dnsmasq, which runs without problem.
br0 is the only interface declared as auto in /etc/network/interfaces.