Single Player: Found weapon/armor upgrades are missing from Weapon Loadout options

Found weapon/armor upgrades are missing in single player (e.g. SMG Ultralight Materials found in Priority: Mars) after being retrieved.

I played through the level OCDish and clearly remember the SMG Scope and Ultralight Materials to be acknowledged by the game as 'found', however I cannot select them in Load out.

I initially dismissed it that maybe I cannot configure the mods until after the mission completion - but since they are still unavailable several missions in, a fix would be necessary.