I'm a very casual player, but I've noticed a few things that I hope the devs will fix soon. They aren't show stoppers, but its kind of wierd.
When my latest character made captain the message read "You are now a Klingon Captain" even though he's a fed character. I am not sure if this wetn for all of his promotions, but hey, devs, that seems like a pretty simple thing to fix to me.
One thats a little more complicated is the mission (forgot the name) where you have to cure the romulan colony of some kind of virus. All of the inflicted romulans are in fact, Starfleet personnel. I don't know if anyone has ever mentioned this to the devs before, but it seems like an obvious mistake. Its a romulan colony...how come the only romulan is the mission contact? Considering how freaking long it takes to kill a romulan medic I'd expect to see some actual romulans there.
I'm sure there are other minor bloopers in game. Its just something I'df like to see fixed for the sake of immersion. (Well, that and the dozen spawn camping NPC ships that give you a community beat down when you enter a DSE But thats a thread in its own and a dead horse thats been beaten to bone dust)