It's a bug that was caused by a change to the quest system a while ago. The quest numbers were changed, and I missed to change the quest number for the command to mark the quest step as done. It shouldn't happen anymore in the newest update, but if the quest was started before the issue was fixed, than it's possible for people to be "beyond" the fixed part already in their saves.
I added a command to the door of Akai's workshop to mark the quest as done for people with this issue. It'll be uploaded with the next release.