The marine side of the game with it's command structure can only be described as chaotic. We can't count on the individual player to fully understand their role or even play their role. Just because a PO was not experienced enough t either lock his doors or check his dropship before taking off shouldn't punish the rest of the shipside crew. I'm not saying shipside Xenos are a bad thing, but they are an incident that requires great coordination to handle if the Xeno player is somewhat competent.
The biggest issue with organization in the game is that communication is difficult. To speak with someone you need to stop moving to type, and the other player needs to read your statement in the chat. We can't fight and type or even walk. Our command is supposed to handle this aspect of communication, but usually that performance ends up falling short due to the same reasons it does on the ground.
What I'm trying to say is that some mechanical changes need to be made to compensate for the fact that it is difficult for people to communicate.