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 mental institution, and leaves a year later.
When Lisa is at the counter ordering her sundae, and she goes to lick the cherry, her tongue is already red from previous takes.
Susanna often writes quotes from other characters in her journal. In one scene, we see her write the quote "If you lived here you'd be home by now", but this quote is not said by Daisy until later in the movie.
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.
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 Susanne 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.
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 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.
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 is getting into the cab on the way to Claymoore the audience sees a weeping cherry tree with pink blossoms in the background. When she gets to Claymoore there are Halloween decorations on the walls and shortly afterwards it's Christmas. Weeping cherry trees only bloom in March or April in North America.
Susanna walks past a Robert F. Kennedy campaign yard sign as she leaves her house to go to the mental hospital. It is fall 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.
At the 1968 party after Susanna and Lisa are picked up in the microbus, The Doors' "Roadhouse Blues", released in 1970, is playing.
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.
When Susanna is first being driven by taxi to the asylum, we see an all blue mailbox through the window. In 1968, mailboxes were red on top, blue on bottom. They weren't painted all blue until the 1970s.
When Susanna is walking through her house during the party, there are extras there. In the background, you can hear, "Look, there's Winona Ryder".
Within the first week that Susanna was admitted to the Mental Institution, there is a scene where she is 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 she has written on, showing the words: "If you lived here, you'd be home now." These are words spoken by Daisy later on in the film when they are at the ice cream parlour. Susanna wrote those words in her diary, because Daisy had said them, and they had made an impact on her. 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.