I've been installing 2 of the same aug on a ship by double clicking the stack from the unequipped items view.
More often than not the 2nd time I try to equip the aug something else random gets unequipped instead of the 2nd aug being equipped. Energy, shield, etc.

This is a initial click issue I believe where the inventory doesn't take note which one you clicked first so it assumes the previous item clicked is the one you want to alter. Will push this to another developer who has more access.

Thanks! I'm not sure what the bug you mentioned is exactly. What's happening for me is if you imagine the augs in this picture are unequipped then trying to equip them both - the 1st one works, then the 2nd one just unequips a random item in inventory.

I'm not sure if it's related but sometimes the client crashes at this point too.