Thanks for the bug report, all. I've already got this in our database, and hope it'll be fixed soon.
I don't know if this will help you at all, but it seems like the NPC ship swap for me is always a Cardassian Battleship. It may be a coincidence but I had just recently played a community authored mission where the last ship I battled was a Cardassian Battleship.
Got another instance of this. In the beginning of "The Longing" there should be a Noble Class contact in the Noro System. Instead it is the generic cruiser from the exploration missions.
Yeah, and I was wondering why you did that.
In my Scavenger Patrol mission, I also set up a few enemy ship groups and set them up with different ship costumes (Generic Frigates, Freighters and the new Vulcan vessel) - and now they suddenly show as the Terran Empire ships they are "under the hood".
Similar custome changes on ground maps don't seem to cause any issues.
Likewise, I tried to run through my missions to make sure everything works as it's supposed to and all the npc contacts I've placed are the generic cruiser, including a group of federation shuttles which, needless to say, looks a little odd in context with the ship they came from