The Times of India is quoting something that they were told by the investigating officer, presumably some sort of police officer.
The investigating officer first tells TOI what the student told the police. This statement is told in normal past tense. Then he tells TOI what the accused's daughter told the police. This statement is also told in normal past tense. In between those two statements, the investigating officer felt the need to explain how the daughter came to be at the police station. As he was now relating something that had happened before the statements had been made, the investigation officer fell back to the past perfect tense.
The past perfect tense is often used to indicate that an event that occurred in the past happened before some other event that happened in the past. So the use of this tense tells us that the order of events is:
1/ The accused's daughter came to the police station with the student, then
2/ The daughter and the student made a report to the police.
Presumably, the student and the daughter were interviewed separately, but we cannot tell form what is written if they both made statements at the same time, or one made a report before the other.