Can't believe it took me so long to find out how to find the "secret" Layer 3 quests.... 

There are a few hidden cubes out there that you can still collect!

It's incredibly easy to do. 

All you do is find a top cube collector on the leaderboard and review the quest history they've completed. There will likely be some you missed which haven't closed but which aren't listed in the normal areas of the UI. 

Good luck!

Since some folk have asked when you're on a user profile, scroll down their quest history and you will see YOUR status of each quest they did. A few will show up as incomplete (but STILL completable)....