Seems to be because new dnsmasq (2.56+, http://www.thekelleys.org.uk/dnsmasq/CHANGELOG) checks if there is junk on its parameters and NetworkManager is sending bogus conf-file.
Related part from nm source: http://cgit.freedesktop.org/NetworkManager/NetworkManager/tree/src/dnsmasq-manager/nm-dnsmasq-manager.c#n278
Also I tried to run dnsmasq without bogus conf file and with, here are results:
juho@juho:~$ sudo dnsmasq --keep-in-foreground
^Cjuho@juho:~$ sudo dnsmasq --keep-in-foreground --conf-file /tmp/sdfsdf.conf
dnsmasq: junk found in command line
juho@juho:~$ sudo dnsmasq --keep-in-foreground --conf-file=/tmp/sdfsdf.conf
dnsmasq: cannot read /tmp/sdfsdf.conf: No such file or directory