I have created a bootable USB drive and followed instructions to set up a LUKS-encrypted partition on the drive. I boot from this drive on a laptop that also has a LUKS-encrypted partition on its main SSD (Qubes is on there). I select "encrypted persistence" from the boot menu.

During the process I was prompted to enter a password for partition /dev/sda2. This immediately seemed wrong to me since I was expecting /dev/sdb3, or certainly /dev/sd*3 since the LUKS partition on the USB drive is the third one. I tried to use the password for the LUKS partition on the USB drive anyway, but it failed with the message "There was an error decrypting /dev/sda2 ... Retry? [Y/n] no key available with this passphrase."

I booted Kali from the USB drive without persistence and I was able to confirm that the USB drive is /dev/sdb. I was also able to manually mount /dev/sdb3 at that point. It seems clear to me that the boot process is trying to access the wrong partition for some reason.