Comment 4 for bug 1879146

I am assuming you messed up string for telling initramfs using the keyfile:

# Deploy keyfile.
echo 'KEYFILE_PATTERN="/etc/luks/*.key"' >> /etc/initramfs-tools/conf-hook

You want to setup luks-encryption so you need address 'cryptsetup':

Edit: "/etc/initramfs-tools/conf-hook" into "/etc/cryptsetup-initramfs/conf-hook"

Resulting to:

# Deploy keyfile.
echo 'KEYFILE_PATTERN="/etc/luks/*.key"' >> /etc/cryptsetup-initramfs/conf-hook

Regenerate initrd:

update-initramfs -u -k all

You should not get 'cryptsetup: WARNING...' and after rebooting you should get asked for passphrase just once. Let me know if it is working that way.