Re: Hostkey wasn't verified!
Can you show your code and attach a relevant session log file?
Before posting, please read how to report bug or request support effectively.
Bug reports without an attached log file are usually useless.
Can you provide more details on "when I run from C# application"? Are you using WinSCP .NET assembly or running WinSCP executable directly?
Some of these may help you:
https://winscp.net/eng/docs/faq_hostkey
https://winscp.net/eng/docs/scripting#hostkey
https://winscp.net/eng/docs/scripting#configuration
https://winscp.net/eng/docs/faq_scheduler