I'm probably reading this wrong, but if you have a aptitude twice you pick a characteristic that shares with an Aptitude. Does the new aptitude have to be paired to something you already possess or is it open to any of the non-charactistic aptitudes? Ogryn that gain toughness for aptitudes from Die Hards get a new aptitude, the only aptitude they can get from the characteristics they possess is Finesse. Or say if I'm making a Bone 'Ead can I take change the extra Tough to say Knowledge?

You're misunderstanding it - it says you get to swap it for an Aptitude that shares the name of a Characteristic. In the case of the Ogryn from a Die Hard regiment, it'd mean you could swap the 2nd Toughness aptitude for say… Weapon Skill, or Strength, or Agility, or any other Aptitude sharing the name of a Characteristic that he didn't have.

So for an Ogryn his choices would be Agility, Intelligence, Perception, Willpower, or Fellowship as he does not normally have those. Non-characteristic aptitudes would be right out.

Exactly so, yes.