Can someone explain this quest? Do I need to fully upgrade 2 manufactories? I upgraded 1 once but it didn't work and I can't skip this quest (I would, because the reward is not worth it).
There is indeed a problem with this type of quest, as announced here. Thank you for reporting, we'll have to wait for a fix now! As far as we can see now, when you are online when the upgrading finishes, it counts towards your quest and when the upgrade finishes while you're not in the game, it doesn't.
This issue is affecting all quests that ask you to upgrade x many buildings. As it was also reported here, and has now been forwarded to the developers for fixing, I'm setting this thread to duplicate and archiving it. Please see the thread I linked, or the announcement Marindor linked for further information on this issue.