Sorry to say, but this will always happen. There's no way for us to make the client loot a specific item forcefully (we tried that in the past, and it led to bans/flagging issues).
Basically, when the bot is trying to loot an item, sometimes the input action carries through longer than we want, so the client "double loots" stacked items. This is due to how the game works.
At best, we'll have some logic later that will drop items in your inventory that don't belong, but for now, that's why it happens.