If this is a non-root pool which is not available at boot, then you should do 
sudo zpool set cachefile=none POOL

That will inhibit the creation of a zpool.cache file for that pool.

The other option, if this is always plugged in, would be to configure it
to unlock automatically on boot. For example, using a key file. This
would be secure only if the root file system is also on LUKS.

** Changed in: zfs-linux (Ubuntu)
       Status: New => Incomplete

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  Ubuntu 16.04 breaks boot with wrong zpool.cache

Status in zfs-linux package in Ubuntu:

Bug description:
  Having just upgraded Ubuntu 16.04, and seeing systemd updates, I
  rebooted the machine, but it failed to start, entering emergency mode.
  Relevant piece of info was this:

  * Failed to start Import ZFS pools by cache file.
  * Started Mount ZFS filesystems
  ** A start job is running for dev-disk....

  and then it enters emergency mode.

  Now, the only ZFS pool I have is a backup USB HDD which is constantly
  attached, and the pool is on a LUKS provider, meaning you won't see it
  until the provider is unlocked.

  My guess is that the latest update, having triggered initramfs
  rebuild, wrote the zpool.cache file with that state, and it shouldn't

  This is totally wrong, as zpool cache should not be built like this as
  it PREVENTS you from having external pools that might not be available
  on boot. I also have no idea why it happened now because I've been
  having this setup (external backup zfs pool on a LUKS provider) since
  16.04 came out and never had a problem until now.

  Removing the /etc/zfs/zpool.cache allowed the system to reboot fine.

  # lsb_release -rd
  Description:  Ubuntu 16.04.1 LTS
  Release:      16.04

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