So I have noticed only recently that the skill mods move to stash when you move an entire loadout to Stash.
To achieve this I had to switch to a different loadout first and then move the first loadiut and if a mod is part of this second loadout it would not move. This is understandable and makes sense.

But the problem is when your skills on second loadout are different. In my example I switch from Hive to Seeker mine. The mods that sit into my Hive did not move with loadout because technically they are still equipped. Even though they are equipped in an unequipped skill.

Pretty simple bug but it becomes a real trouble. May be you can address this sooner than later.