When you launch Citrix AppCenter / Configuration Tools / Hotfix Management, the console won’t list any installed hotfixes present on the machine.
Also, when you try to create a new Hotfix list from the action pane, no hotfixes are found.
This problem is not new, but persists in Xenapp 6.5.

In order to get the hotfix management functional, you need to change the permissions on the following registry key

(note that this is the 64bits key path, as it appears under the Wow6432Node key, for 32bits installs it would just be listed under HKLM\Software\Citrix\ProductCodes)

Open Server Manager and verify under which account the IMA Service is running.
By default this will be Network Service.

Add this account to the registry key permissions and give Full Control rights.

As soon as you reopen the console, you will see the list of installed hotfixes and be able to create a new hotfix list based on the locally installed ones.