Cam hands Hodgins the folder when they are trying to figure out what the weapon was and she has her hands on her hips but in the next scene she is holding the folder again.
When Brennan is looking at the bones for the first time she is looking down but in the next scene she is looking slightly up and to the right.
When Booth is talking in the diner he has his right hand up and his left on the table but in the next scene he has both hands up now.
Just because two priests went to the same seminary does not mean a thing. It would only matter if they were there at the same time.
Bones repeatedly says she could have gone with Sully to sail in the South Pacific. Sully was very clear that he was heading from DC to the Caribbean and never mentioned any plans to head to the Pacific.