In the episode with the 14 yr old male victim (The Ghost in the Machine (2012)), Brennan said she was uncomfortable determining sex off of a skull, but in this episode she finds the victim to be a Caucasian male, just because of his prominent brow ridge.
Hodgins identifies the insects as webworms. In reality, the insects used were mealworms (a beetle larvae rather than moth larvae). Actual webworms resemble caterpillars with soft green colored bodies, and most species are fuzzy. Whereas mealworms are brown with a smooth hard exoskeleton as seen in the show. Mealworms were most likely used due to their commercial availability and cheap price point.
When bringing in birds to eat the web worms, Hodgins identifies them as crows when they are actually young ravens.
The publisher talks about an accessible way for the public to be introduced to archaeology, Bones then holds up a book about fossilized dinosaur eggs - the study of dinosaurs falls under palaeontology NOT archaeology (which is specifically the study of humans). This is a very common mistake.
Dr Edison is describing how his site contains both Homo Sapiens and Neanderthal, and Bones dismisses this. It has been known for years before this episode was written that Homo Sapiens and Neanderthals interbred. Given the two co-existed for thousands of years it would not be unheard of to have a site with mixed remains.
You cannot tell the sex of a 3 year old just from their bones.
Bones claims that a bone sticking to the tongue is a clear indication that the bone is human. While bones do stick to the tongue and this practice is not common but well known as a way to distinguish between bones and non-bones (e.g. rocks), animal and human bones are not different from each other and cannot be distinguished that way.
Bones claims that Peek-a-boo "demonstrates an infant's ability to understand object permanence", while developmental psychologists argue that peek-a-boo demonstrates an infant's inability to understand object permanence. (Mayers, "Exploring Psychology", 2011) Sweets also seems to be misunderstanding the developmental significance of the game, both when trying to get Christine to play and later when briefly talking about the game with Booth. Without the understanding of object permanence, an infant will assume that anything it can't see, after a short period of time, no longer exists. The game relies on the surprise and excitement of the infant of having something it recognizes suddenly appear out of nowhere. Consequently, the fact that Christine is not entertained by this simple game is evidence that she has already fully grasped the concept of object permanence and is not entertained by the game because she knows that the other player's face is simply hidden behind their hands. Bones should have expected this and been playing the game earlier since her child was repeatedly mastering other tasks beyond her age group's expectations.
Despite the spelling, the word 'Neanderthal' is pronounced 'Neandertal', as if the 'h' wasn't there.
Booth and Bones both claim that bleach cannot be used to remove blood. While chlorine based bleach indeed does not remove blood evidence, it removes it enough to not be detected without special hemoglobin detection chemicals and oxygen bleach does prevent detection even using chemicals.
Throughout the script several character refer to individual skeletons as "homo sapien", as if "homo sapiens" were a plural form. The characters are sufficiently well educated not to make that mistake. Even the IMDB submission checker recognises it.