These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Freud Was Right: Poor Charlie. Upon seeing his sister in the bathtub as a child, was struck by her (seeming) lack of genitalia. Not only did he come to the conclusion that their parents removed it to punish her, but his mother caught him and...jumped to the wrong conclusion. This earned him a traumatic experience with a knife and a deep-seated fear that he'd be castrated one day as well. Anytime he tries to have sex, bam! Traumatic memories.
Some Anvils Need to Be Dropped: The book is very clear that the treatment of the mentally disabled by abled people is horrific. Things actually have improved in the treatment of the developmentally disabled since then - and probably at least partially as a result - In the 1950's it was very common for families to send away these folks. Nowadays its more acceptable to have a special needs child.
The Woobie: Charlie, obviously. Realizes that his so-called friends were simply using him as a toy, finally reaches genius levels of intelligence, only to lose it, and starts to forget almost all the notable events that happened to him towards the end.