Some Loopholes in the G.I.Joe Movie

The 80s G.I.Joe movie was kind of fascinating at first for me when I was little, however I've noticed that the movie had a LOT of loopholes like:

• Has the whole Cobra Command been demoted by the usurper Serpentor? For example at the beginning, Cobra Commander is the one who sets the bomb up yet when he shouts retreat, they all still obey his command.  
  
• When Cobra Commander and Serpentor have a battle of words, only the highest command attacks Cobra Commander, the rest are just silent yet we see a lot of them.  So what are they for?  Has Cobra Commander failed to call the rest?  Cobra Commander is NOT that stupid.  I mean he's been making plans in the past that really worked like Megatron did.
• Serpentor says he'll face the intruder by himself yet in the process, he crawls into a hole, something that Cobra Commander would do. Also how could Cobra-La install into his memories bits and pieces of his origin?  I find it funny.
  
• It seems that Cobra Commander, Dr. Mindbender and Destro were demoted altogether. We see them on a Cobra jeep without the Cobra sign with Dr. Mindbender being in charge of firing the lasers while Cobra Commander drives, Destro does nothing at all. What the?! Also even if he was demoted, they all still follow his command to retreat proving that he was still the highest next to Serpentor even if they were all demoted.
• So Cobra-La hates humans? But then why did Golobulus have Dr. Mindbender create Serpentor from some of humanity's most evil dictators? Don't tell me Karl Marx was a member of Cobra-La too?  Also, why did the rest of Cobra still go on with the plan especially if they have relatives who could also devolve in the process?
• So who died or just went missing? After the movie, DIC bought the rights to G.I.Joe and the Operation Dragonfire series reveals that Serpentor is alive and well, he has Destro, Baroness, Zarana and a new recruit named Gnawhyde while Cobra Commander still remains a snake. So did Dr. Mindbender, Zartan and the Crimson Twins die in the dome? It's not left explained how some of them survived.
• Duke's injury is questionable. He was bitten by a poisonous snake near his heart, considering that it's a vital organ. It would make sense if he died. However complaints caused the script to be changed to the point Duke returned in the second DIC season.