During at least one of tonight's skirmishes in Deneb I was automatically grouped with the Itani. I am KOS with Itani and admired with Serco, and I took the mission from a Serco station. This caused confusion more than once when I was chatting with my group only for us to realize we were attempting to kill each other.

It may be relevant to say that I'm UIT faction, but not sure why or how that would matter.

Something else that is somewhat related to this is the assassination mission that is available to me, which would have me kill one bot from each of my enemies. There are a couple of issues with this: 1) it is a UIT mission that is available to me from Serco stations and 2) it is asking me to kill Serco (and Itani) bots due to them being what the mission says are enemies of the UIT. As far as I'm aware that isn't actually the case... the UIT isn't (officially) on the side of either the Serco nor the Itani, so how could either be regarded as enemies?

Did you join the Itani military or the Serco military? I'm pretty sure you have to choose and you can only choose that once or any character.

iirc the Assassination mission asks you to "liquidate two high priority targets", meaning that the hit could be financially motivated, instead of politically. This makes sense in the case of the UIT, where cutthroat business tactics are a way of life.