Ok here's the bug.
Bug,
When accessing Loot Crates (any flashing box that you can get Hypos and whatnot from) in Instances;
If you don't have enough room for all the incoming loot in your Pack, that loot will be lost, since you don't get a second chance to activate the crate again.
Ok so
Location,
I've only just noticed it in the Romulan epesoids, but I bet that this bug encompasses far more missions than these alone.
Way to repeat bug
1. Loot a Crate while having a full Inventory with nothing that matches the incoming loot's signatures (your bags are full of everything but the new items, so none of them will stack.)
Alright that's about it then.
Hope this helps