Everything looks OK from a log point of view, I’m seeing exactly what I expect to see:
9:41:53 Info | Purging the directory 'C:\****\****'
19:41:53 Info | Leaving files and directories that match any of: 'App_Data\*, Media\*, Downloads\*'
19:42:09 Info | Copying package contents to 'C:\****\****'
19:42:09 Info | Copied 3106 files
Is it possible for you to try and replicate the issue with another release (if you have a test environment that you can check against).
As for the error you are seeing:
19:42:30 Error | Cannot create a file when that file already exists. (Exception from HRESULT: 0x
19:42:30 Error | 800700B7)
19:42:30 Error | At C:\Octopus\Work\20180515160821-9834-188\Script.ps1:11 char:1
19:42:30 Error | + $webSite.Start()
19:42:30 Error | + ~~~~~~~~~~~~~~~~
19:42:30 Error | + CategoryInfo : OperationStopped: (:) , COMException
19:42:30 Error | + FullyQualifiedErrorId : System.Runtime.InteropServices.COMException
That is IIS reporting that you have multiple sites bound to the same port, more information on how to resolve that can be found here.
I hope that helps, please let me know if there is anything else we can assist with, and please let me know if you are able to replicate your initial issue,