The Organon hymn being such a central melody in the trilogy—playing during the main menu for example—makes sense in retrospect, since the three most central characters to the game are prototype Organon.
It's never confirmed in the game, but given that Lady Goal had no problems with tics in Donna's body, it's entirely possible Donna's behavior is a result of an improper brain implant.
Why didn't Argus notice Rufus while he was trapped in the interrogator, even though he was behind a transparent dome at waist height? As seen before with the Shop-O-Mat, the people of Deponia have great difficulty in noticing people trapped under transparent domes.
You don't think much of it at the time, but upon further reflection the explanation that Hermes likes to play around with clones' hair colors, and that colors change during puberty, only explains why Goaly has a different hair color from the adult Donna. It does not explain why Donna's first corpse wound up with Goal's hair color. Hermes has no reason to change it and Argus didn't know that Rufus had been thrown back to the surface (and survived), so it couldn't be him setting a trap either. This is lampshaded in the Developer commentary.