Revealing mistake: In the scene of Tod's death when we see the water leak creeping up toward him, if you look closely you can see the small holes in the tile grout where the water is being pumped up from below.
Revealing mistake: You can see the plane intact even though it has exploded. It stays complete, there's just fire around it. (00:18:55)
Revealing mistake: In the scene where Carter drives madly down the road to get to Alex, and Billy is riding his bike along the street, just before Billy gets knocked off you can clearly see it is a stunt double.
Revealing mistake: When Alex is running through the woods and is sliding down the hill, just before he stops himself from being impaled by some branches, you can hear someway say "Look out." It can't be the agents following as they're too far away.
Answer: The scene where Terry was killed was most likely shot during the day. It is quite common for film makers to film a scene during the day to get the right lighting effects and then later CGI the night sky and the proper shadowing. This is most effective when you have an area that would otherwise be too dark or have environment that wont allow for the proper lighting for a night shoot. As for the bus, your guess is as good as mine.