I know its quite late for an answer, but following is theThe 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"
}