Is this sentence correct?
Why is the coach substituting Ronaldo? Who is coming on instead?
my problem is "on" Is it a part of the phrasal verb ("come on") or it's a preposition for "instead"? or it's incorrect entirely?
This sentence is correct -- it may seem rather confusing, because the sentence in question is shorthand. "Coming on," in this case, is short for "coming onto the field." As a full sentence, this would read:
Why is the coach substituting Ronaldo? Who is coming onto the field in his stead?
Basically, all the second question is asking is who will be replacing Ronaldo on the field.
It is correct. 'on' goes with 'coming'. This means 'who is coming here/joining (us) instead'. Let's wait for other answers.