ONLY A NON-TEACHER'S OPINION
(1) "A number of" = many. So that's why "people" is the subject.
(2) "Fifty percent" does NOT = many.
(a) Thus we could analyze it as:
Fifty percent (subject) + of the people (prepositional phrase) + are coming (verb
phrase). (The number of the verb -- singular or plural -- depends on the object of the
preposition."People" is plural.)
Fifty percent (subject) + of the cake + has been eaten. ("cake" is singular.)
Fifty percent (subject) + of the jury (collective noun) is/are women.
("jury" is a collective noun. It can be a unit or different individuals:
The jury has given its decision; The jury are arguing very loudly.)