Consider the following scenario:
You install Cumulative Update 5 (CU5) for Microsoft BizTalk Server 2016.
You download a file from the SFTP server.
Due to long time taken for message processing, the receive location shuts down.
In this scenario, the file is downloaded again when the location restarts which causes file duplication.
Microsoft has confirmed that this is a problem in the Microsoft products that are listed in the "Applies to" section.
This problem is fixed in the following cumulative update for BizTalk Server:
Cumulative Update 6 for BizTalk Server 2016
For information about the service packs and cumulative update list for BizTalk Server, see the following article in the Microsoft Knowledge Base:
2555976 Service Pack and cumulative update list for BizTalk Server
For more information about BizTalk Server hotfixes, see the following article in the Microsoft Knowledge Base:
2003907 Information about BizTalk hotfixes and Cumulative Update support