Make sure the file being written to the FTP folder is completely written before it gets picked up by BizTalk as some FTP servers do not lock files and BizTalk starts picking them up before they’re finished being written: you can do this by changing the source system to write the file with a different extension and after writing renaming it to an extension that the BizTalk receive location is monitoring.
Also, if you have two BizTalk servers as hosts of the host instance of FTP adapter receive handler you should cluster the host so that only one of the host instances is running at once.