Hi @Alex_404 - Welcome to MS QnA, and thank you for posting here!
I'm not sure exactly what kind of SFTP server you're running, but based on my findings, this issue can happen if your SFTP server has its
ExtractableCount setting set to
1 which is usually its default value: https://www.ibm.com/support/pages/message-extractable-count-set-1-default
If you locate this setting in your SFTP server configs and are able to change it, can you increase it to 3 (or 4?) and then try running your Logic App workflow again?
The SFTP-SSH connector works well when a higher value is set for the
ExtractableCount setting on the SFTP server side, especially, If you have chunking enabled and/or processing large files. Also, note that Logic Apps uses different operation sequence from WinSCP, so the two have different behaviors. I hope this is helpful, let me know if any questions :)