For some reasons when retrieving the ID of a content type at the list level in PowerShell, the ID of the parent content type (i.e. the one at the site level) is always returned.

Below is my script:

$web = Get-SPWeb http://myServer
$list = $web.Lists.TryGetList("My List")
$contentType = $list.ContentTypes["My Content Type"]
$contentType.ID

Running the above script would give me:

Notice the property being displayed is Parent. I have no idea why it is doing this.

To get around this, I get the content type ID from its SchemaXml property by changing the script to be:

$web = Get-SPWeb http://myServer
$list = $web.Lists.TryGetList("My List")
$contentType = $list.ContentTypes["My Content Type"]
[xml] $contentTypeXml = $contentType.SchemaXml

$contentTypeXml.ContentType.ID

This then gives the expected result as below:

This behaviour was observed on SP2013 without any PU or CU applied.