The biggest one (as noted under Paranoia Fuel) is that the house could be haunted, or the characters could be just getting scared by loud noises.
Eleanor's line "Nature's Mistakes" could refer to a bigoted view of homosexuals...or it could refer to people with extrasensory perception.
The "are you married?" exchange could mean that Theo is in a romantic relationship with a woman...or it could mean she's living with a man out of wedlock. Theo specifically refers to her partner as "we." A rather careful gender ambiguity. Especially considering the taboo on homosexuality at the time.
Theo's angry reaction to Luke's flirtation could mean that she's not attracted to men...or it could mean that she's offended by his familiar behavior and finds him disrespectful.
Theo's annoyance/anger at Markway's compliment about Nell's perception could mean that she's feeling jealous about a good looking man paying attention to the girl she likes... or she could feel that he's slighting Theo's gift...OR she's reacting badly to Markway's attentions to Nell because she knows he's married; she's hoping her chilliness toward Markway will rub off on Nell. Then perhaps Nell won't get attached, and get hurt.
As seen in Les Yay below, one interpretation of Nell's behavior towards Theo going along with the "Theo is a lesbian" theory, in the way that Nell alternates between coldness and warmth to Theo, is that Nell herself is also a lesbian and her internalized homophobia is another cause of her mental instability. When she calls Theo "one of nature's mistakes", she's both fighting off her own attraction and projecting her own bigotry onto Theo.
Les Yay: It is more or less universally accepted that Theo had a crush of some sort with Nell. A lot of the things she says to Nell come as very flirty, and a lot of her actions can only be explained as her being jealous of Nell and Dr. Markway becoming closer. Not to mention, her making fun of Nell also comes as some manner of teasing.
Consider the amount of time that Nell spends holding hands with Theo, snuggling up to her in bed, and begging her to stay close. Not to mention how tightly the two of them are gripping each other when they're hiding in horror from the banging on their door. Or how comforted Nell is when she thinks that Theo is holding her hand. Or how she affectionately reaches out to wrap a blanket around Theo when the latter is cold. Or how offended Theo looks when Nell calls her "one of nature's mistakes..."
Confirmed, at least on the director's end about Theo. There was originally going to be a scene where Theo was screaming curses at someone out the window of her apartment while "I Hate You" was written on the mirror in red lipstick, making it about as clear as possible for the period that Theo had just broken up with her lover and was making herself available to Nell.
Values Resonance: The movie is arguably not only ahead of its own time, but ahead of ours. At a time when mental illness was usually used in film either as a Freudian Excuse for the villain, or to make a character completely helpless, this movie shows Nell as a strong woman trying to take control of her own life. However...
Values Dissonance: Considering how she drives into a tree, dies, and might or might not have been trapped forever in the house as a ghost it could be argued that she failed spectacularly at doing so, rendering the whole point moot. Even in the ending Dr. Markway implies that the stress of the house was too much to bear for her and she finally cracked. Not exactly the most positive showcase of mental illness.