TL/DW: Loot boxes have a chance at spawning on top of one another. Only so many loot boxes can spawn in an area. In Game Settings you can set Interaction Mode to “always highlight” to make this more obvious.

Some Issue council tickets to upvote to help it grab CIGs attention:
https://issue-council.robertsspaceindustries.com/projects/STAR-CITIZEN/issues/STARC-183802
https://issue-council.robertsspaceindustries.com/projects/STAR-CITIZEN/issues/STARC-182806
https://issue-council.robertsspaceindustries.com/projects/STAR-CITIZEN/issues/STARC-177988