I have the similar issue, but I'm using OpenVPN and the symptom is
slightly different.

With OpenVPN, the name resolution is normal on the first attempt to
connect VPN (after reboot). However, by disconnect and connect VPN
again, the name resolution will be broken. As below.

== Reproduce steps ==
1. Reboot system
2. Connect to OpenVPN gateway
3. Issue command "host server.mydomain.com" -> success
   DNS request & response can be seen by sniffing (Wireshark) tun0 interface
4. Disconnect VPN
5. Connect to OpenVPN gateway
6. Issue command "host server.mydomain.com" -> Host server.mydomain.com not 
found: 5(REFUSED)
   DNS request & response can NOT be seen on tun0 nor ens33 interface

Note A: After step 6, DNS resolution will NOT back to normal unless
reboot or "sudo service network-manager restart".

Note B: After step 6, logout and login will NOT make it back to normal.

Note C: After step 6, issue command "host server.mydomain.com 192.168.3.74" -> 
success, assume 192.168.3.74 is the DNS server behind VPN gateway
DNS request & response can be seen on tun0 interface

== Package information ==
libnma-common                  1.2.6-0ubuntu0.16.04.2
libnma0:amd64                  1.2.6-0ubuntu0.16.04.2
network-manager                1.2.6-0ubuntu0.16.04.1
network-manager-gnome          1.2.6-0ubuntu0.16.04.2
network-manager-openvpn        1.1.93-1ubuntu1.1
network-manager-openvpn-gnome  1.1.93-1ubuntu1.1
network-manager-pptp           1.1.93-1ubuntu1
network-manager-pptp-gnome     1.1.93-1ubuntu1
resolvconf                     1.78ubuntu4

It will became NOT reproducible after downgrading
network-manager                1.2.2-0ubuntu0.16.04.3


OS version:
Ubuntu Desktop 16.04.2 LTS amd64

This test is conducted under virtual machine environment to minimise
uncontrollable factors.

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You received this bug notification because you are a member of Ubuntu
Touch seeded packages, which is subscribed to network-manager in Ubuntu.
https://bugs.launchpad.net/bugs/1671606

Title:
  DNS server from vpn connection is not being used after network-manager
  upgrade to 1.2.6-0ubuntu0.16.04.1

Status in network-manager package in Ubuntu:
  Confirmed

Bug description:
  I use my company's cisco vpn via network-manager in Ubuntu 16.04.2
  LTS. After recent upgrade of network-manager:amd64 from version
  1.2.2-0ubuntu0.16.04.4 to version 1.2.6-0ubuntu0.16.04.1 DNS
  resolution of VPN's server hostnames does not work. Roll back to
  version 1.2.2-0ubuntu0.16.04.4 solves the problem.

  Steps for reproducing:
  1. upgrade network-manager:amd64 from version 1.2.2-0ubuntu0.16.04.4 to 
version 1.2.6-0ubuntu0.16.04.1
  2. connect to VPN via network-manager applet
  3. nslookop servername.internal --> ** server can't find servername.internal: 
NXDOMAIN
  4. disconnect from VPN via network-manager applet
  5. roll back network-manager via command: sudo apt-get install 
network-manager=1.2.2-0ubuntu0.16.04.4
  6. restart network-manager via sudo service network-manager restart
  7. connect to VPN via network-manager applet
  8. nslookop servername.internal --> the server is resolved correctly

  ProblemType: Bug
  DistroRelease: Ubuntu 16.04
  Package: network-manager 1.2.6-0ubuntu0.16.04.1
  ProcVersionSignature: Ubuntu 4.4.0-66.87-generic 4.4.44
  Uname: Linux 4.4.0-66-generic x86_64
  ApportVersion: 2.20.1-0ubuntu2.5
  Architecture: amd64
  CurrentDesktop: Unity
  Date: Thu Mar  9 19:49:55 2017
  InstallationDate: Installed on 2015-10-05 (520 days ago)
  InstallationMedia: Ubuntu 15.04 "Vivid Vervet" - Release amd64 (20150422)
  NetworkManager.state:
   [main]
   NetworkingEnabled=true
   WirelessEnabled=true
   WWANEnabled=true
   WimaxEnabled=true
  SourcePackage: network-manager
  UpgradeStatus: No upgrade log present (probably fresh install)
  nmcli-nm:
   RUNNING  VERSION  STATE      STARTUP  CONNECTIVITY  NETWORKING  WIFI-HW  
WIFI     WWAN-HW  WWAN
   running  1.2.6    connected  started  full          enabled     enabled  
enabled  enabled  enabled

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