$FileStream = New-Object IO.FileStream($File.FullName,[System.IO.FileMode]::Open)
                    $FileCreationInfo = New-Object Microsoft.SharePoint.Client.FileCreationInformation
                    $FileCreationInfo.Overwrite = $true
                    $FileCreationInfo.ContentStream = $FileStream
                    if(!($file -match $pat)){
                        $FileCreationInfo.URL = $newfile
                    }else{
                        $FileCreationInfo.URL = $File
                    }
                    $Upload = $DestinationFolder.Files.Add($FileCreationInfo)
                    $Context.Load($Upload)
                    $Context.ExecuteQuery()
                    Write-host "Adding the meta data to the document in O365"
                    $ListItem = $Upload.ListItemAllFields;
                    $Listitem["Modified"] = $ModDateSP
                    $Listitem["Created"] = $DateSP
                    $Listitem["Author"] = $author  
                    $Listitem["Editor"] = $lastSaved  

                    $ListItem.Update()

                    $Context.Load($Upload)
                    $Context.ExecuteQuery()
                    if($Upload.CheckOutType -ne "none")
                    {
                        $Upload.CheckIn("Checked in by Administrator", [Microsoft.SharePoint.Client.CheckinType]::MajorCheckIn)
                    }
                    $output=([System.Uri]$SiteURL).PathAndQuery
                    $folderurl=$output+'/'+$DocLibName+$folderrelativepath
                    $sourcefolder = $Context.web.GetFolderByServerRelativeUrl($folderurl)
  $Context.Load($sourcefolder)
  $Context.ExecuteQuery()
  $Context.Load($sourcefolder.Files)
  $Context.ExecuteQuery()
  foreach($item in $sourcefolder.Files){
    if($item.name -eq $file.Name){
                    Write-host "File Found"
                    $context.Load($item)
                    $context.ExecuteQuery()
                    $Versions = $item.Versions
                    $context.Load($Versions)
                    $context.ExecuteQuery()
                    write-host $Versions.count
                    }
                    }

I have this code above which uploads a file changes the metadata checks it in and then counts the versions of the file.

The problem is when I count the versions it does not contain any saying the version count is 0 but when I go into the document library and check the versions manually there are 2.

This is annoying because I am trying to delete the first version and as it is not finding any versions I cannot do this.

Any ideas?

This is by design. There is the file creation, upload, and setting of the properties (property promotion), so the version will never be at 1.