A crew member on Vincennes, who originally identified the plane as civilian, complained it was so dark in the operations area that he could not read the (paper) listing of civilian flights.
Crew on deck with binoculars (or perhaps even without, at only 11nm) would have seen what it was; there would be no way to combine that knowledge with a blip on the screen in a dark control room.
The same would apply to MH17. The locals standing outside would have known it was a civilian craft on a normal route where they regularly see these. The guy at the dark enclosed SAM controls would see only a blip.... heading his way from the west, where all the previous danger has come from.