Only one document is indexed

My filebeat agent has the monitoring section configured to send logs every 5s, directly to an elasticsearch cluster dedicated only for logs monitoring.
However, only one document is indexed at midnight during the rollover of the .monitoring-beats index.
No error appears in the filebeat log. We can see that documents are well gathered.
When I try to send to an another elasticsearch server, it works fine.
Need any help or suggestion to figure out why this behavior.