Playing 2.3.8 (Just noticed that 2.3.9 was out, but it's probably not relevant). I have had a few iterations of this level where an enemy transport comes into the northeastern Nexus mini-base, may or may not drop off its units, but then just sits there at ground level. Unfortunately, when this happens, I don't seem to be able to make the mission complete and go to the next one. The transport seems essentially indestructible (well, after 20 minutes of game time of 8 assault gun units, 8 TK units, and probably some 20-30 heavy artillery units/emplacements (ripple rockets, ground shakers, and hellstorms I couldn't tell if I'd made a dent in it) and I'm not sure if the mission won't complete because of the unresolved enemy unit, or if there's something else going on.
Keith