Same story here,
mounting aufs over sqashfs on /usr breaks boot, relevant /etc/fstab entries:

/.filesystems/usr/usr.sqfs /usr squashfs ro,loop,nodev 0 0
aufs  /usr  aufs  br:/.filesystems/usr/overlay=rw:/usr=ro  0 0

The workaround, I have to life for a while, is to #comment aufs,
after boot, un-comment, "mount -a", comment. Not that sane.

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multiple entries in fstab with same mount-point
https://bugs.launchpad.net/bugs/503003
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