Got to about 67% done on the Faction Rally Milestone and it disappeared on me.
Edit: Confirmed that on completion, you receive 16 Faction coins without a 'Milestone Complete' Message. So if it disappears, you most likely completed it.
-
Same thing happened to me - Milestone just disappeared. Went to the Dead Orbit vendor to see if it could be turned in, but there's nothing to turn in. Really irritating.