After you complete the "Do no Evil" quest, it is possible to find a crate containing an elite clue using your Ava's Alerter. You need a spade to this, and you can only do it once. I think there are more locations than the 4 I'm providing, but that are not currently known. I found mine on lunar isle. I think this is worth adding into the rewards section, or tips & tricks section.

 

Hope this helps

 

South west part of lunar isle:

 

 

Elven lands, right after you exit the underground pass:

 

 

The iceberg faced in the penguin quests(cold war, hunt for red raktuber):

 

In Meiyerditch:

I have not done the quest, but I have heard that there was a 5th location that no one has been able to determine.

Indeed, for some of our crew members none of the locations listed yielded an elite clue. We're hesitant to put up an incomplete list, so please bear with us...