$absentStudent=0;
$index=0;
foreach ($allStudents as $std) { //all students

    $absenties=0;
    $rollNo=$std->roll_no;

    foreach ($allDailyAttendance as $attend) { //all daily info
        $attendanceInfo=$attend->id;
        $attendance=StudentAttendance::all()->where('attendance_info',$attendanceInfo);
        foreach ($attendance as $stdAttend) {
            if(($stdAttend->roll_no == $rollNo) AND ($stdAttend->attendance=='a'))
            {
                $absenties++;
            }
        }
    }

    if($absenties >= 2 )
    {
        ++$index;
        $absentStudent = array( // $absentStudent is replaced by each loop
        // instead, you should push new value to $absentStudent
            $index => array(
                'rollNo' => $rollNo,
                'absents' => $absenties
            )
        );

    }
}

// Example:
        $absentStudent[] =
            array(
                'rollNo' => $rollNo,
                'absents' => $absenties
            )
        );