I've been using the Duty Officer system for a few weeks now and some of my officers are definitely picking up negative traits, is it because they have taken part in failed missions or is the system totally random and officers will just pick up negative traits for no particular reason please?
I have not notice and changes to Doff traits, but I have only been Doff'ing since mid January.
Generally speaking, there are no inherently "bad traits" that Doffs have. A trait is "bad" depending on the nature of the mission. A trait that is perfectly good for one type of mission may have bad consequences or no effect at all in another mission.
For example, take Doctor X who is Emotional and Peaceful.
Mission #1 is to treat another Doff in sickbay for stomach pains. The Emotional trait could be useful for a Critical Success. The fact that he is peaceful, do not have any affect. Being a doctor helps when you treat a patient so it increases your success of properly diagnosing the cause of the pains and applying treatment.
Mission #2 is an way mission giving support to ground troops in a front line situation. Being a doctor is a good thing if you are going to give medical support, just for that it increases your chances of success. However, having the Peaceful trait would be bad because he may feel that fighting can be completely avoided if both sides are simply willing to talk, therefore he may not even want to be on this mission at all. Thus having the Peaceful trait contributes to Failure for the mission. The fact that he is Emotional could be a Critical Fail because that can mean his reaction when under fire is unpredictable.