In both the text and the film of "Flowers for Algernon" Charlie saves Algernon from being dissected after he dies because he cares to much about Algernon to have that happen to him. Buried him and put flowers on his grave.
In the movie, Dr Burt replaces Dr Nemur from the book
In both the book and the film Charlie gets surgery on his brain to get smart. He was chosen for the surgery because he wanted to come a genus.
Unlike the movie, Charlie never meets his mom in the book
In the text ans the film Dr Strauss shows Charlie off because charlie is a living example of his research.
Charlie's "friends" laugh at him in the movie
In the short story "Flowers for Algernon" the character Dr Nemur is the is the Scientist that works with Charlie through the months as he is getting smart and in the film Dr Burt plays that role instead of Dr Nemur.
In the film version of "Flowers for Algernon" Charlie has a very emotional scene where he talks to his mother for the first time. Since he was a kid and finds out why she sent him away. and in the text version that never happened. His mom was never a character in the text.
In the film version of "Flowers for Algernon" Charlie realizes that his so called friends weren't actually his friends as they were only talk to him for their own amusement, he learns this a lot faster then in the text version.