Plot hole: The government would have no chance of hiding the existence of the comet for a year. Most comets are discovered when they are very faint, literally thousands of times fainter than Wolf-Beiderman when Leo found it. Long before the events in the film take place, probably even before the government itself would be notified, the comet would have been discovered, an orbit calculated, and people panicked. The whole premise of the first half of the movie is thus based on flawed logic.
Plot hole: The time and distance of the movie doesn't make sense. The comet was only 3.7 million miles away from Earth when the Messiah mission failed. That is about 1/10th the distance to Mars. They should have been able to put more contingency plans into place. Also, it took the Messiah 5 months to reach the comet which means it was only going 1,033 mph, which is very slow for spacecraft.