I've reproduced this in a vm (more or less, my timestamps are different
but still wrong, but I'm guessing that's just due to different timezone
configurations).

Some relevant entries from /proc/mountinfo:

24 26 8:1 / /media/root-ro ro,relatime shared:2 - ext4 /dev/sda1 ro,data=ordered
25 26 0:20 / /media/root-rw rw,relatime shared:3 - tmpfs tmpfs-root rw
26 0 0:21 / / rw,relatime shared:1 - overlayfs overlayroot 
rw,lowerdir=/media/root-ro,upperdir=/media/root-rw//overlay,workdir=/media/root-rw//overlay-workdir
101 26 0:43 / /home/ubuntu rw,nosuid,nodev,relatime shared:80 - ecryptfs 
/home/ubuntu/.Private 
rw,ecryptfs_fnek_sig=8123544c12013d26,ecryptfs_sig=de2cdf716df70cde,ecryptfs_cipher=aes,ecryptfs_key_bytes=16,ecryptfs_unlink_sigs

So, the original root is mounted at /media/root-ro, and there's a tmpfs
at /media/root-rw which holds the overlayfs work and upper directories.
/ is an overlayfs mount, and the encrypted files for my homedir are
stored in /home/ubuntu/.Private (which is a symlink to
/home/.ecryptfs/ubuntu/.Private).

What I see is that only the files in the root of the ecryptfs mount
which come from the lowerdir have incorrect timestamps. A directory I
created before enabling overlayroot has the correct timestamp, and two
files in that directory also have correct timestamps. New files created
in the directory (which thus exist only in the upperdir) have the
correct timestamp, however if I modify a file created before overlayroot
was enabled the timestamp remains incorrect, and even does so if I
remove and create a file of the same name.

The timestamps in /home/.ecruptfs/ubuntu/.Private are all correct. I'm
guessing that ecryptfs takes timestamps from the lower directory inodes,
so my hunch is that this is a problem in ecryptfs.

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https://bugs.launchpad.net/bugs/1636890

Title:
  invalid file times with overlayroot and encrypted home

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