as part of https://bugs.launchpad.net/ubuntu/+source/mdadm/+bug/1722491
there is currently mdadm update available from xenial-proposed and
zesty-proposed that might resolve this issue.
To test that solution please perform the following:

1) Install mdadm from xenial-proposed/zesty-proposed
   - See https://wiki.ubuntu.com/Testing/EnableProposed
   - Or download & install packages from
xenial
https://launchpad.net/ubuntu/+source/mdadm/3.4-4ubuntu0.1/+build/13596415
zesty
https://launchpad.net/ubuntu/+source/mdadm/3.3-2ubuntu7.5/+build/13596431

2) $ sudo apt install dracut-core

3) $ sudo systemctl enable mdadm-shutdown.service

4) $ sudo systemctl start mdadm-shutdown.service

After this the expectation is for shutdown/reboots to perform clean a
shutdown, maintaining the raid array in a synced state, such that it
comes up clean.

Please let me know if above resolves shutdown/reboot issues for you.

Regards,

Dimitri.

** Changed in: mdadm (Ubuntu)
       Status: Confirmed => Fix Committed

** Changed in: mdadm (Ubuntu Xenial)
       Status: Confirmed => Fix Committed

** Changed in: mdadm (Ubuntu Yakkety)
       Status: Confirmed => Won't Fix

** Changed in: mdadm (Ubuntu Zesty)
       Status: Confirmed => Fix Committed

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https://bugs.launchpad.net/bugs/1608495

Title:
  IMSM fakeraid handled by mdadm: unclean mounted volumes on
  shutdown/reboot

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