When Lisa is at the counter ordering her sundae and goes to lick the cherry, her tongue is already red from previous takes.
When Susanna is meeting with the psychiatrist in the beginning of the movie, the same black car drives by twice. The same cars are parked in the same places when she enters the Claymoore and when she leaves a year later.
When Susanna is taken by taxi to the asylum, at first her luggage is on her right. After the flashback, she is sitting on the right side.
Susanna often writes quotes from other characters in her journal. In one scene, she writes the quote "If you lived here you'd be home by now", but Daisy doesn't say this until later in the movie.
Angeline Jolie, who has natural blue eyes, wears brown contacts in the film. When Lisa is recaptured after her jaunt in Florida, her bright blue eyes can be seen when Susanna sees her face through Lisa's locked room-viewing portal.
In the film, Susanna is diagnosed with Borderline Personality Disorder but it did not exist as a diagnosis in the DSM II, which was the diagnostic manual that was published in 1968 when the film is set. Borderline Personality Disorder was not a formal diagnosis until the DSM III, which was published in 1980.
We see Susanna being given sedatives/sleeping pills at the institution. They begin to take effect within seconds. This is possible with an injection of the drug, but never with a tablet that is swallowed.
"The End of the World" by Skeeter Davis is on Daisy's record player, but the record itself is a Columbia 45 from the early-to-mid-1950s (red label, gold print). This song was first released on an RCA 45 from 1963 with a black label.
The girls in the hospital are shown watching The Wizard of Oz (1939) during the daytime. In the 1960s, "The Wizard of Oz" was only broadcast once a year, around Easter, and only during the evening. Since this movie takes place before the availability of the VCR, there's no way they could have been watching this movie during the day, but since recording devices of the type did exist at that time, and since the original work was not a linear story, it could be that they could simply have it in a different format.
In the taxi when Susanna first goes to Claymoore, she lights a cigarette. Then she jumps into a flashback. When the flashback is over, she lights a cigarette again. There is no sign of the cigarette before the flashback. Given how long the real-time might have taken during the flashback, it's entirely likely that she finished the first, got rid of it, and lit a second.
The slits on Daisy's wrist do not appear until Lisa pulls up her robe sleeve. When she asks for the Valium and her wrist is exposed, there are no cuts at all.
As Susanna gets into the cab to go to Claymoore, a weeping cherry tree with pink blossoms is in the background. When she gets to Claymoore, the walls sport Halloween decorations, and shortly afterwards it's Christmas. Weeping cherry trees only bloom in March or April in North America.
At the 1968 party after Susanna and Lisa are picked up in the microbus, The Doors' "Roadhouse Blues"--released in 1970--is playing.
Susanna walks past a Robert F. Kennedy campaign yard sign as she leaves her house to go to Claymoore in autumn 1967. Kennedy didn't announce his intention to run for president until March 1968.
The story shows the draft lottery taking place before Martin Luther King Jr. is assassinated. King was assassinated in 1968, and the first draft lottery was in December 1969.
When Susanna is talking to an employee at her high school about her plans for college and her career, she says she's not going to burn her bra, drop acid, or march on Washington. The bra burning story was published in 1968, not 1967 when Susanna was in high school.
The front of a 1969-model Chevrolet appears in a street scene, prior to the news story about the assassination of Dr. Martin Luther King, Jr which was April 4, 1968. A 1969 Chevrolet would not have been available until late-summer 1968.
When Susanna is walking through her house during the party, extras are there and someone clearly says "Look, there's Winona Ryder".
During Susanna's first week at Claymoore, there's a scene of her lying on her bed writing in her diary, moments before Lisa sneaks in and scares her. The shot of her writing in her diary reveals a page which s shows the words: "If you lived here, you'd be home now." Daisy speaks these words later on in the film when they're at the ice-cream parlor' Susanna wrote these words in her diary because they had made an impact on her when Daisy said them--proving that those words should not have been written in her diary, as Daisy had not spoken them yet.
When Lisa is ordering a sundae at the ice cream counter, she asks for "sprinkles", which are known as "jimmies" in the Boston area.