This issue is tracked here:
https://winscp.net/tracker/1977

Thanks for your report.
I have sent you an email with a debug version of WinSCP to the address you have used to register on this forum.

Semi-randomly getting this message as a pop-up in WinSCP when closing a session, opening, and reconnecting to server:

Remote side sent disconnect message type 11 (by application): "Bye Bye"

It doesn't happen with every server I have tested but more than one, and running different software. I have eliminated any network or system issues. It seems like there isn't anything actually going wrong but just interpreting wrong or maybe the closing sequence is off. The server that I am mostly running into issues with is running Robo-FTP (have tried multiple versions). I'm getting the error on recent versions of WinSCP, this doesn't happen on 5.15.
In WinSCP log i see the following sequence:

Closing connection.
Sending special code: 1
Remote side sent disconnect message type 11 (by application): "Bye Bye"
(ESshFatal) Remote side sent disconnect message
type 11 (by application):
"Bye Bye"

Nothing indicating errors on server log.
Any help would be greatly appreciated.