I think you want $data[$category] = $question;
Or in case you want an array that maps categories to array of questions:
$data = array();
foreach($file_data as $value) {
list($category, $question) = explode('|', $value, 2);
if(!isset($data[$category])) {
$data[$category] = array();
}
$data[$category][] = $question;
}
print_r($data);