Record with duplicate external id was inserted through bulk API upsert

Question

1. I have Account with user id as external id.
2. I have a record of Account with user id 123 created 2 months ago.
3. I have an upsert job created through bulk API yesterday with user id as externalIdFieldName. It was trying to upsert Account with user id 123 and all the other fields.
4. It turns out that another Account with user id 123 was created by the upsert job

Question: why another Account was created instead of updating the old record with user id 123? From my understanding, the upsert job will lookup the records with the external id. If it find one matching, it will be updated; otherwise, a new record will be created.

So in this circumstances, why a duplicate record could be created?

Code to create Bulk upsert job:

$params = array(
    "externalIdFieldName" => 'User_ID__c',
    "object" => 'Account',
    "operation" => 'upsert'
);
$path = "/services/data/v41.0/jobs/ingest";
$c = curl_init();
curl_setopt($c, CURLOPT_POST, 1);
$encodedParams = json_encode($params);
curl_setopt($c, CURLOPT_POSTFIELDS,$encodedParams);
// url will be look like csxx.salesforce.com/services/data/v41.0/jobs/ingest
curl_setopt($c, CURLOPT_URL, $this->host . $path);
curl_setopt($c, CURLOPT_CONNECTTIMEOUT, $this->connectTimeout/1000);
curl_setopt($c, CURLOPT_RETURNTRANSFER, 1);
$header = array('Content-type: application/json', 'Authorization: Bearer '. $this->sessionId);
curl_setopt($c, CURLOPT_HTTPHEADER, $header);
data = curl_exec($c);