You are correct, not running atleast wipefs before using luksFormat on
the block device was a mistake on my part, but I barely remember making
it. I half expected fsck to come up with some errors, so I let it make
changes. It is not a volume that is always connected at startup, hence
the manual check. It was just the wrong block device. An isLuks check
would have returned yes and prevented fsck from running. Maybe libblkid
could detect luks partitions?

This happened on a 2 drive raid 1 array, which I have dd backups of, if
some how the array can be recovered. Hard lesson learned though. Thank
you for the explanation.

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https://bugs.launchpad.net/bugs/1713175

Title:
  Obsolete backup ext2/3/4 superblocks can confuse e2fsck on an
  encrypted LUKS partition

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