Hi!
This is most likely due to an unfortunate momentary desync between any two of the game servers, our backend system, and your end. I'm real sorry about the trouble. l can try and compensate you for your losses with some valuable lootbags. Do let me know what your in-game account name is, and which of your characters this happened with! 

As for minimizing the risk of this happening, as per one of our most experienced players, Schalimah:

• Try to keep inventory interactions to the bare minimum while on mission.
• Best case you shouldn't open your inventory at all in missions.
• If you are full, delete items whithout sorting your inventory.
• Empty your inventory before supreme missions.
• Use loot filters to not pick up low quality gear in the first place.