Right after updating to NetworkManager-1.4.0-1.1, it failed to update /etc/resolv.conf saying that it had been manually modified, which it wasn't. Removing /etc/resolv.conf fixed the issue and NetworkManager works as expected again, generating the right /etc/resolv.conf file.

Log messages complaining about /etc/resolv.conf being manually modified:
...
sep 24 21:41:47 Apidell avahi-daemon[1726]: Registering new address record for 10.10.80.105 on wlp12s0.IPv4.
sep 24 21:41:47 Apidell NetworkManager[1728]: <info>  [1474749707.7739] device (wlp12s0): state change: secondaries -> activated (reason 'none') [90 100 0]
sep 24 21:41:47 Apidell NetworkManager[1728]: <info>  [1474749707.7740] manager: NetworkManager state is now CONNECTED_LOCAL
sep 24 21:41:47 Apidell NetworkManager[1728]: <info>  [1474749707.7772] manager: NetworkManager state is now CONNECTED_SITE
sep 24 21:41:47 Apidell NetworkManager[1728]: <info>  [1474749707.7775] policy: set 'Dynamode10' (wlp12s0) as default for IPv4 routing and DNS
sep 24 21:41:47 Apidell dns-resolver[12458]: ATTENTION: You have modified /etc/resolv.conf. Leaving it untouched...
sep 24 21:41:47 Apidell dns-resolver[12460]: You can find my version in /etc/resolv.conf.netconfig
sep 24 21:41:47 Apidell NetworkManager[1728]: <13>Sep 24 21:41:47 dns-resolver: ATTENTION: You have modified /etc/resolv.conf. Leaving it untouched...
sep 24 21:41:47 Apidell NetworkManager[1728]: <13>Sep 24 21:41:47 dns-resolver: You can find my version in /etc/resolv.conf.netconfig
sep 24 21:41:47 Apidell NetworkManager[1728]: ATTENTION: You have modified /etc/resolv.conf.  Leaving it untouched...
sep 24 21:41:47 Apidell NetworkManager[1728]: You can find my version in /etc/resolv.conf.netconfig ...
sep 24 21:41:47 Apidell NetworkManager[1728]: nisdomainname: you must be root to change the domain name
sep 24 21:41:47 Apidell NetworkManager[1728]: nisdomainname: you must be root to change the domain name
sep 24 21:41:47 Apidell NetworkManager[1728]: <warn>  [1474749707.9942] dns-mgr: could not commit DNS changes: Error calling netconfig: exited with status 20
sep 24 21:41:47 Apidell NetworkManager[1728]: <info>  [1474749707.9943] device (wlp12s0): Activation: successful, device activated.
sep 24 21:41:47 Apidell dbus[1705]: [system] Activating via systemd: service name='org.freedesktop.nm_dispatcher' unit='dbus-org.freedesktop.nm-dispatcher.service'
...

/etc/resolv.conf contents that NetworkManager refuses to overwrite:
# Generated by NetworkManager
<<EOF

/etc/resolv.conf contents after former file is removed and NetworkManager reconnects to the network:
### /etc/resolv.conf file autogenerated by netconfig!
#
# Before you change this file manually, consider to define the
# static DNS configuration using the following variables in the
# /etc/sysconfig/network/config file:
#     NETCONFIG_DNS_STATIC_SEARCHLIST
#     NETCONFIG_DNS_STATIC_SERVERS
#     NETCONFIG_DNS_FORWARDER
# or disable DNS configuration updates via netconfig by setting:
#     NETCONFIG_DNS_POLICY=''
#
# See also the netconfig(8) manual page and other documentation.
#
# Note: Manual change of this file disables netconfig too, but
# may get lost when this file contains comments or empty lines
# only, the netconfig settings are same with settings in this
# file and in case of a "netconfig update -f" call.
#
### Please remove (at least) this line when you modify the file!
nameserver 192.168.11.1
nameserver 10.10.80.1
<<EOF