The case
The whisper in the corn is the engine of the movie, and it says "he." The film is about Ray Kinsella's father, and the singular pronoun is the whole point of the ending.
"They will come" is what the line became once it left the movie and turned into business advice. Build the product, the customers will come. The plural version is used so often that it replaced the original in memory.
Why our brains do this
A movie line that becomes a proverb gets reworded for the proverb's meaning, and the proverb version circulates far more than the film.
Sources: Wikipedia — Field of Dreams · Wikipedia — False memory: the Mandela effect
