Booth says the body has been washed ashore. A few seconds later, we see scuba divers emerging from the water and carrying the body towards the shore.
(at around 15 mins) The group is talking about salt water and fresh water with the fish. Booth states that there is only "salt water" at the marina and that there is no "fresh water" nearby. However, we are told earlier the body was found on the Chesapeake Bay near the south-western area around Grafton, VA. That area of the Chesapeake Bay is composed of fresh, brackish, and salt water due to the three large fresh water rivers that empty into it. So, not only was the water more than likely brackish due to it being near the edge but there are three large rivers (the James, the York, and the Rappahannock) and several smaller ones, that could be the source of fresh water.
In the scene where the team is stabbing the dummy to determine the amount of force each person exerts, they repeatedly state that they are measuring the force in Newton-meters. However, a Newton-meter (a.k.a. a Joule) is a unit of energy, not force. They could be measuring the force in Newtons, but not Newton-meters.
In the car when Brennan and Booth discuss a bible story, Brennan says "Even an empiricist can have a heart Booth" the camera focuses on Booth, Brennan is heard talking but her mouth does not move.
The team determines from particulates in the victim's body that she had been dumped in the Rancocas Creek in New Jersey and washed down the Delaware River in a flood, and from that deduces that the murder had taken place in Gloucester City, New Jersey. The creek that empties into the Delaware at Gloucester City is the Big Timber Creek; the Rancocas Creek empties into the Delaware at the town of Delanco, approximately twelve miles upstream from Gloucester City.
(at around 2 mins) In the opening sequence Booth says that "the body washed up in the bay" and then a moment later Bones and Booth are shown driving west across the national mall (away from the Chesapeake Bay) as Bones says that taking "the I-70" will be faster. The I-70 runs west, and away from the Chesapeake Bay, out of Baltimore Maryland (approximately 40 miles north) and the I-270 is the spur just outside of Washington D.C. that connects to it, but that would take you northwest and also away from the Chesapeake Bay.