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I know its quite late for an answer, but following is the PowerShell code which can be helpful to remove ITEM content type from custom list.

    Add-PSSnapin "Microsoft.SharePoint.PowerShell"
    $web = Get-SPWeb "UrlOfYourSite"
    $list = $web.Lists["YourListName"]
    $ctToRemove = $list.ContentTypes["Item"]
    if($ctToRemove)
    {
        Write-Host "Removing Item content type"
        $list.ContentTypes.Delete($ctToRemove.Id)
        $list.Update()
        $Web.Dispose()
    }
    else
    {
        Write-Host "Item content type do not exists in list"
    }

I hope it helps!!