The Escaping Freighters have alien skins, but have Federation Ship names. The ones I fought was a Miranda, Intrepid, and a Destiny-class. Also, showing with Federation Icon (not sure if this is supposed to be or not).
Was doing patrol mission and was on 90 percent of the mission. When fleet alert pop up. Hoped in, finished it. When i finished it. It took it i was doing patrol and finished the patrol mission . Which i wasnt doing . And now i cant turn to mission to starfleet to collect me reward .
EDIT : ok, little addition. You can turn mission when you are in space sector, But not from Hail starfleet