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.
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.
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.
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 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.
In the scene where Toby visits Susanna at Claymoore, Valerie escorts him to the television room. Toby and Susanna talk briefly, with Janet observing them nearby in the background, on the left. When both Toby and Susanna exit the room, Janet suddenly appears on the right side.
In the film, Susanna is diagnosed with Borderline Personality Disorder but it did not exist as a diagnosis in the DSM II, which would have been the diagnostic manual used during 1968 when the film is set. Borderline Personality Disorder was not a formal diagnosis until the DSM III which was released in the 1970s.
"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.
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.
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 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.
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.
The goof items below may give away important plot points.
Incorrectly regarded as goofs
Polly supposedly doused herself in gasoline to get rid of the rash that her new puppy had given her. The probability that she wouldn't be allergic to the cat at the end is highly unlikely. Most people with dog allergies are even more allergic to cats. The book indicates that Polly setting herself on fire was a suicide attempt; the dog story coming from a pathological liar.However shown when the group reads their files it shows clearly that it wasn't that she tried hurting herself it says on the headline of the news it was a fire in the 6th grade that caused her to look as deformed as she was
Lisa asks Daisy if there is a tub, Daisy replies no. When Daisy Kills herself she is clearly hanging in front of a tub. As Daisy has been portrayed as a notoriously difficult and selfish girl, she could have just been saying she didn't have a tub so that Lisa wouldn't try to use it.