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.
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.
Values Resonance: The movie is arguably not only ahead of it's 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.