When Chuck is falling from the roof, John uses his left hand to catch Chuck by his left hand too. Chuck is also holding the Cipher in his right hand. In the close-up shot it is two right hands. Or two wrong hands, for the matter :)
In the last episode of Season One, Big Mike's fish was put back together with duct tape and hung back up on the wall. In the first episode of Season Two, Big Mike's fish is hanging in his office undamaged and intact.
How did Casey have his Crown Victoria back ? He lost it when it blew up after he gave Chuck the cords so the missile from the launcher had a new target to explode.few episodes back .
(at around 13 mins) Chuck is talking to Ellie about his first date, and in the background at the breakfast bar you can clearly see a crew member.
Sarah arrives at Chuck's house to let him know that the new intersect computer has blown up literally within 10 seconds after it happens (which happens save his life in the last second). It would have taken a lot longer for her to find out about it, head to Chuck's house and let him know.