By my reading, both sides agree that the girl's efforts to make the boy stop were essentially limitted to the utterances "I should be going now" and "I need to go home"; the article doesn't make clear the time between these statements, but suggests that both sides agree intercourse continued for about 90 seconds after the first was issued. The issue before the court is whether the utterance of such statements is sufficient for a girl to revoke her consent.
If this were a 'he said/she said', and she'd claimed she told him clearly and unambiguously to "STOP IT!" there would have been no basis for appeal. The defense's appeal here is on the basis that even if every fact claimed by the prosecution were true the conduct alleged would not merit the prescribed charge.