The mistakes are quite obvious, so hopefully easy to fix
The AI has been awful since BB1, and hasn't improved much since, and Cyanide have shown little to no inclination to improve it, nor add tools to allow the community to do so.
For example, your point #1 has been reported since BB1 was in beta-testing (if not alpha-testing), so the fact it's still there should tell you something.
Secondly, now you need to bear in mind that an Apothecary can be used in two separate instances - one instance is the injury table (the one that determines if they are knocked down, stunned, KO'd, injured) -
I think this is where your confusion is stemming from - as per the Apo rules dode posted above, the Apo is not used on the Injury roll (stunned, KO'd, Casualty), only on the KO or Casualty itself.
The Apothecary allows you to re-roll the Injury roll (the D68), not the Casualty roll (the 2D6).
- So your opponent rolls armour (breaks) - you can do nothing about this.
- Your opponent rolls for injury (2-7 Stun, 8-9 KO, 10-12 Casualty) - if it's a KO you'll be offered the use of the Apo here to turn it into a Stun.
- If your opponent gets a casualty, the roll a D68 for type of injury - after this, you will be offered the use of the Apo, which will give a reroll of the D68, ten you can choose which to accept.
- If either of the casualty rolls (original or reroll) is a Badly Hurt (and chosen) then the player is moved to the Reserves section of the dug-out.