Yup, this was it. Noteworthy: Augmentation Kits must be in personal inventory, unlike most (all?) other crafting materials for other crafting.
Well the thing is, an MK-6 augment kit is not a crafting mat. Its a crafting schematic, its more similar to a biochem stim or a cybertech grenade, in other words, a single-use item. Therefore, it makes more sense to have it in your inventory before using it, as you cannot use stims or grenades from your cargo hold
That being said, it should be reported as a bug that it shows you can use it on the screen