In the mission, in which this happened to me, the first two enemies I spotted, both had loot on them.

One of them (a Viper), after it had already been damaged by a Sniper shot, which I took at the start of the turn out of concealment; I killed with a critical sword attack. Because my Ranger ended up in the loot-recovery zone, the loot from the Viper was correctly, automatically retrieved.

The Second Enemy, an Advent Stun Lancer in low cover, was, in the same turn, initially damaged by a frontal shot from a Specialist and subsequently killed by a second shot from another Specialist, which had flanked the Stun Lancer.

The Stun Lancer correctly dropped a second loot cache.
This second loot cache was instantly retrieved in error.
The closest of my units to the Stun Lancer was, with a distance of 7 Tiles, the same Ranger, that had killed the Viper and recovered the first loot cache.

TL;DR: killing multiple enemies with Loot and retrieving one of the loot caches, may recover all of the loot caches. This is a bug.