Bones fails to realize that reality TV doesn't really reflect reality. When Angela tries to explain this, Bones' response is, in essence, that it must be Exactly What It Says on the Tin. It's supposed to be a cute example of Bones' naivete. But anyone who has taken even Anthropology 101 (like this troper) learned about how people behave differently when they know they're being observed, and that's just when some academic type is sitting quietly to the side taking notes. Bones, as an anthropologist, should have realized that a camera and the prospect of fame and money would increase this effect by orders of magnitude.
Bones' blithe belief that nobody in the middle of a prison riot would hurt a pregnant woman, which Booth rightly points out is nonsensical. For one thing, there are enough prisoners in general population that may very well have been guilty of violence against women, even if they weren't convicted specifically for them, that betting on nobody being willing to take a shot at a pregnant woman is statistically unlikely. But even assuming that the entire riot was full of people who would never hit a woman (let alone a pregnant one) intentionally, riots are inherently chaotic melees. All you need is one person not aware of everything around them, and Bones very well could have received multiple hits. Plus, the guy she was chasing was in prison - they very well could have waited for the warden to get the riot under control before going after him, as it's not like he was going anywhere. Not to mention she has worked many cases in which the bodies she has examined are that of murdered pregnant women. Making it even more ridiculous she has no ability to comprehend that there are people (many in prison) who are capable of harming a pregnant woman.
Vincent's habit of spouting random facts as a blatant sign of his social awkwardness, does that remind you of anyone we know? No wonder Bones told him that he was her favorite intern when he was dying. The only real difference is that Vincent is far more blatant about it.
Somewhat a fridge Funny moment when you realize the naming of Christine Angela Booth. her first name means "Christian", her middle name means "angel", and her last name comes from her father who is deeply religious. And her mother is a proclaimed atheist.
Why does Brennan's subconscious pick Wendell as a symbol for Zack in the Season 11 finale? It's because Wendell was the intern present in "The Perfect Pieces in the Purple Pond", Zack's last appearance in real time. It also explains why Dream Wendell has a cigarette behind his ear: he had one in that episode too.
Rewatch The Pain in the Heart.' Angela, Hodgins, and Zack are alone in the hospital room, Zack tries to tell them the truth about the explosion and Gormogon. Unfortunately they think he's delirious from pain and drugs, so they give him morphine and put him to sleep. If they had listened, the team wouldn't spend the rest of the episode accusing each other of being the apprentice, and they might not have lost their standing with the FBI. Doubles as Fridge Brilliance when you remember that the evidence was pointing toward Hodgins at that point. The audience could easily believe that Zack has important evidence to share that may reveal Hodgins' role in the murders, but he's silenced by the morphine first.
Christine probably remembers every detail of the men sent after her and her brother by a vengeance killer after Booth killing the agents protecting her and injuring her grandpa. Here's hoping she copes with this in a healthy manner instead of snapping.
In "Mayhem on a Cross": Brennan's revelation that her foster parents once locked her in the trunk of a car for two days as punishment for breaking a dish is absolutely chock-full of these. Brennan says that she doesn't think it was fair, "even though they gave [her] fair warning." The ever-rational and logical Brennan, on some level, believes that because her foster parents told her that they would lock her in a trunk if she broke another dish, she was "given fair warning" and their punishment was therefore rational. And her comments don't focus on what was done to her, they focus on what she did. The water was so hot, the soap was so slippery, she didn't mean to do it—she's defensive, even though she was the one who ended up in the trunk. She says that they believes they were in the wrong, but her defensive comments indicate that at least some part of her doesn't quite agree that they actually were wrong. The second time she says "the water was so hot"—like she's almost pleading with Booth to understand that she hadn't broken the dish on purpose and not to blame her—is gut-wrenching.
In "The Woman in the Garden": Brennan was kidnapped and mentally tortured for three days by a crew of soldiers during an excavation trip to El Salvador—a trip which happened after she and Angela became friends, and Angela had tried to get her to go to Italy instead. Angela clearly had no idea and looks horrified when Brennan tells her what had happened (and Brennan seems to indicate that she's leaving some things out of her account, which Angela seems to pick up on), but it's also possible that her horror is heavily mixed with guilt. If she had tried a little harder, maybe she could have gotten Brennan to join her in Italy and none of this would have happened. And Angela almost certainly greeted her with her usual cheerful bubbly exuberance when she came back, and had probably talked Brennan's ear off about the wonderful time she'd had in Italy and given her a hard time for not cutting loose and taking vacation time, completely unaware of the horrors her friend had just gone through.
In "The Pain in the Heart": probably just a goof by props, but when Brennan and Booth come to confront Zack, in the background you can see that Zack's heart rate remains perfectly steady, even as he explains setting up the explosion and defends his logic to Brennan. We lose sight of the heart rate monitor once Brennan points out the hole in his reasoning and he realizes how badly he has messed up. But up until that point, Zack is calm and rational, with a perfectly even heart rate, even up against his beloved mentor defending his role in multiple murders. Zack really does believe in Gormogon's reasoning, and at that point may well have committed murder if Gormogon had ordered him to.