Oh, grammar checker...
You try so hard, and you're so wrong so often. (Which is, of course, why I don't have you turned on normally.)
If you questioned it, they looked at you, puzzled, and said ‘don’t you know who’s giving the orders for the program?’What does the grammar checker want done with this sentence? It wants the comma between "it" and "puzzled" turned into a semicolon. Yes. Even though the explanation for this specifically says
If the marked comma is separating two complete but related sentences, replace the comma with a semicolon.(It adds this If the second half of your sentence begins with "then," add "and" before "then." but since there's no 'then' there I'm disregarding that.)
Yes. Apparently the grammar checker thinks
puzzled, and said ‘don’t you know who’s giving the orders for the program?’is a complete sentence.