Visible crew/equipment: A green screen is visible in Agent Weine's glasses when talking to Agent Schrek after they let Alex go during Ms. Lewton's death sequence. (00:58:05)
Visible crew/equipment: When the train breaks Carter's car there is a camera man inside it.
Visible crew/equipment: During the FBI's original investigation, a green screen can be seen in the officers glasses. However, nothing green is in the room. (00:20:50)
Visible crew/equipment: After Alex walks into Ms. Lewton's home before he discovers her blood on the floor, you can see a crewmembers shadow moving on the light brown TV table. (Note the shadow doesn't match Alex's movements).
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.