Hi,
I am also seeing this issue running Alfred 3.2 and macOS 10.12.1. It doesn't occur consistently but roughly once a week - I lock/unlock using alfred 5+ times a day. I am not using lock/unlock via an apple watch. I am entering my password on the lock screen.
When it occurs all the apps relaunch like logging in. In the terminal the command "whoami" returns the correct user name however I am unable to ssh to anywhere afterwards. I receive the error about the user not existing. Sorry I lost the error message in, I will post again the next time it happens. The only way to correct the problem once it occurs is to reboot.
Its almost like its starting a duplicate session of the same user rather then unlocking back into the locked user.
Let me know any other information I can provide. If it keeps happening I will try the screen saver option.
Thanks