I have the same issue when e.g.:
- switching from Ethernet (via a USB-to-Ethernet adapter) and WiFi
- turning on or off a VPN managed by NetworkManager (openvpn configured 
manually does not have the issue)

My current workaround is to killall dnsmasq as root. It will re-start
automatically with the updated settings.

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https://bugs.launchpad.net/bugs/1639568

Title:
  dnsmasq not updated by NetworkManager on system resume

Status in network-manager package in Ubuntu:
  Confirmed

Bug description:
  When the system resumes after sleep dnsmasq is either not updated with
  new dns information of never resumes operation.  Restarting the
  network-manager service will manually resolve the problem.  Everything
  else seems correct, the DHCP information is correct and shows the
  correct nameservers, resolv.conf is updated correctly.  I am unable to
  determine if the issue is with dnsmasq not resuming or if the dbus
  message with the name servers is getting lost.

  ProblemType: Bug
  DistroRelease: Ubuntu 16.10
  Package: network-manager 1.2.4-0ubuntu1
  ProcVersionSignature: Ubuntu 4.8.0-26.28-generic 4.8.0
  Uname: Linux 4.8.0-26-generic x86_64
  ApportVersion: 2.20.3-0ubuntu8
  Architecture: amd64
  CurrentDesktop: Unity
  Date: Sun Nov  6 07:24:44 2016
  IfupdownConfig:
   # interfaces(5) file used by ifup(8) and ifdown(8)
   auto lo
   iface lo inet loopback
  InstallationDate: Installed on 2016-11-03 (2 days ago)
  InstallationMedia: Ubuntu 16.10 "Yakkety Yak" - Release amd64 (20161012.2)
  IpRoute:
   default via 192.168.1.1 dev wlp58s0  proto static  metric 600 
   169.254.0.0/16 dev wlp58s0  scope link  metric 1000 
   192.168.1.0/24 dev wlp58s0  proto kernel  scope link  src 192.168.1.218  
metric 600
  NetworkManager.state:
   [main]
   NetworkingEnabled=true
   WirelessEnabled=true
   WWANEnabled=true
  SourcePackage: network-manager
  UpgradeStatus: No upgrade log present (probably fresh install)
  nmcli-dev:
   DEVICE   TYPE      STATE      DBUS-PATH                                  
CONNECTION                CON-UUID                              CON-PATH        
                                   
   wlp58s0  wifi      connected  /org/freedesktop/NetworkManager/Devices/0  
The_Magical_Mystery_Tour  4e4fe235-20a0-414a-8ec3-97f65060250e  
/org/freedesktop/NetworkManager/ActiveConnection/1 
   lo       loopback  unmanaged  /org/freedesktop/NetworkManager/Devices/1  --  
                      --                                    --
  nmcli-nm:
   RUNNING  VERSION  STATE      STARTUP  CONNECTIVITY  NETWORKING  WIFI-HW  
WIFI     WWAN-HW  WWAN    
   running  1.2.4    connected  started  full          enabled     enabled  
enabled  enabled  enabled

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