So this would be my guess:

The first time you invoked userdel, it removed the user from the system (/etc/passwd, /etc/group, and /etc/shadow) but didn’t delete the home folder because according to lastlog the user was still logged in. When you invoked it a second time, it failed because the user no longer exists – after all, it deleted the entries from the various system files. Which left you with all the files in the home folder …

Either way, this sounds like a problem with userdel which, if you can recreate it, needs to be reported as a bug.