User blog comment:Suparockr/List of Plotholes throughout the series/@comment-2250460-20120719024024/@comment-1221773-20120719032114

Who says the cutscene is showing Leng's ship being tracked in real time? It's noted throughout the games and books that while travel from relay to relay is near-instantaneous, traveling between relays in a system can take much longer, even hours, despite FTL. We don't know how much time elapsed between Leng's escape from Thessia and Shepard seeing the hologram of his journey to Horizon, so it's entirely possible that Leng had the time to make a pit stop at Cronos Station before continuing on to Horizon.