We seem to hit the same problem here.

Can you post you NetworkManager.conf file ? if it was not upgraded
correctly that could be the issue

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https://bugs.launchpad.net/bugs/1782679

Title:
  systemd-resolved can't resolve at all, need to add nameservers to
  resolve.conf

Status in systemd package in Ubuntu:
  Confirmed

Bug description:
  I'm running Ubuntu 18.04 (upgraded from 17.10) on a machine with both
  ethernet and wifi interfaces. When I boot, my ethernet connection
  enp0s31f6 is brought up by Network Manager and given three nameserver
  addresses via DHCP, 10.1.13.10, 10.1.141.10, 10.1.13.36. Running nmcli
  shows the three nameservers under "DNS configuration". Running
  "systemd-resolve --status" shows them under a "Link 2 (enp0s31f6)"
  section. I can do a "ip route get to X" and ping each one
  successfully. No other connection is active.

  testuser ☼ systemd-resolve --status
  Global
            DNS Domain: orgsdomain.net
            DNSSEC NTA: 10.in-addr.arpa
                        16.172.in-addr.arpa
                        168.192.in-addr.arpa
                        17.172.in-addr.arpa
                        18.172.in-addr.arpa
                        19.172.in-addr.arpa
                        20.172.in-addr.arpa
                        21.172.in-addr.arpa
                        22.172.in-addr.arpa
                        23.172.in-addr.arpa
                        24.172.in-addr.arpa
                        25.172.in-addr.arpa
                        26.172.in-addr.arpa
                        27.172.in-addr.arpa
                        28.172.in-addr.arpa
                        29.172.in-addr.arpa
                        30.172.in-addr.arpa
                        31.172.in-addr.arpa
                        corp
                        d.f.ip6.arpa
                        home
                        internal
                        intranet
                        lan
                        local
                        private
                        test

  Link 3 (wlp4s0)
        Current Scopes: none
         LLMNR setting: yes
  MulticastDNS setting: no
        DNSSEC setting: no
      DNSSEC supported: no

  Link 2 (enp0s31f6)
        Current Scopes: DNS
         LLMNR setting: yes
  MulticastDNS setting: no
        DNSSEC setting: no
      DNSSEC supported: no
           DNS Servers: 10.1.13.10
                        10.1.141.10
                        10.1.13.36
            DNS Domain: orgsdomain.net

  However, when I actually try to resolve a name, even the name of one
  of the nameservers, dig claims that "connection timed out: no servers
  could be reached".

  testuser ☼ dig dcpdc001.orgsdomain.net +nocookie

  ; <<>> DiG 9.11.3-1ubuntu1.1-Ubuntu <<>> dcpdc001.orgsdomain.net +nocookie
  ;; global options: +cmd
  ;; connection timed out; no servers could be reached

  Note that this name should resolve to 10.1.13.10, the first
  nameserver. The "+nocookie" option is there to work around an issue
  with Windows DNS servers. But other than that, the servers themselves
  work fine if I tell dig where to look:

  testuser ☼ dig dcpdc001.orgsdomain.net +nocookie @10.1.13.10

  ; <<>> DiG 9.11.3-1ubuntu1.1-Ubuntu <<>> dcpdc001.orgsdomain.net +nocookie 
@10.1.13.10
  ;; global options: +cmd
  ;; Got answer:
  ;; ->>HEADER<<- opcode: QUERY, status: NOERROR, id: 61294
  ;; flags: qr aa rd ra; QUERY: 1, ANSWER: 1, AUTHORITY: 0, ADDITIONAL: 1

  ;; OPT PSEUDOSECTION:
  ; EDNS: version: 0, flags:; udp: 4000
  ;; QUESTION SECTION:
  ;dcpdc001.orgsdomain.net.      IN  A

  ;; ANSWER SECTION:
  dcpdc001.orgsdomain.net.   3600    IN  A   10.1.13.10

  ;; Query time: 2 msec
  ;; SERVER: 10.1.13.10#53(10.1.13.10)
  ;; WHEN: Fri Jul 20 10:56:27 AEST 2018
  ;; MSG SIZE  rcvd: 65

  I have configured resolvconf to use dynamic updates. /etc/resolv.conf
  points to /run/resolvconf/resolv.conf. This file contains only (non-
  comments):

  nameserver 127.0.0.53
  search orgsdomain

  If I add "nameserver 10.1.13.10" to this file manually, suddenly dig
  can resolve again (without the @...), and anything else that needs to
  resolve names can do so. Removing the nameserver breaks that again.

  I don't know much about the servers. They're part of a Windows-based
  network, but since I can use them if I edit resolv.conf or give dig
  the address, I don't think they're the issue (except in the sense that
  maybe they require a feature that systemd-resolved doesn't support?).

  I increased the logging level of systemd-resolved to "debug" and
  "journalctl -f -u systemd-resolved" shows this during a failed query:

  Jul 20 10:33:23 heerij-ubuntu systemd-resolved[2352]: Got DNS stub UDP query 
packet for id 19836
  Jul 20 10:33:23 heerij-ubuntu systemd-resolved[2352]: Looking up RR for 
dcpdc001.orgsdomain.net IN A.
  Jul 20 10:33:23 heerij-ubuntu systemd-resolved[2352]: Switching to DNS server 
10.1.13.10 for interface enp0s31f6.
  Jul 20 10:33:23 heerij-ubuntu systemd-resolved[2352]: Cache miss for 
dcpdc001.orgsdomain.net IN A
  Jul 20 10:33:23 heerij-ubuntu systemd-resolved[2352]: Transaction 12728 for 
<dcpdc001.orgsdomain.net IN A> scope dns on enp0s31f6/*.
  Jul 20 10:33:23 heerij-ubuntu systemd-resolved[2352]: Using feature level 
UDP+EDNS0+DO+LARGE for transaction 12728.
  Jul 20 10:33:23 heerij-ubuntu systemd-resolved[2352]: Using DNS server 
10.1.13.10 for transaction 12728.
  Jul 20 10:33:23 heerij-ubuntu systemd-resolved[2352]: Sending query packet 
with id 12728.
  Jul 20 10:33:23 heerij-ubuntu systemd-resolved[2352]: Processing query...
  Jul 20 10:33:23 heerij-ubuntu systemd-resolved[2352]: Timeout reached on 
transaction 12728.

  This repeats dozens of times, trying the other nameservers too. Note
  that there is substantially less than a second between the "Processing
  query..." message and the "Timeout reached..." message. (There are
  also problems with the other servers not having port 53 open, so I
  also get "Using degraded feature set..." messaged for them. But again,
  the first server seems to work fine with everything except systemd-
  resolved.)

  Things I have tried:

    * Enabling DNSSEC. It's supported, but doesn't fix the issue.
    * Explicitly setting nameservers in Netplan's config. Is accepted, but 
doesn't change anything.

  Sorry for the lack of the usual bug report attachments, but getting
  anything out of this machine and on to the internet is now a massive
  pain. Let me know what other debugging info might help and I'll try to
  add it.

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