After installing Web Interface the following error may be seen:

Server Error in '/' Application.
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Runtime Error 
Description: An application error occurred on the server. The current custom error settings for this application prevent the details of the application error from being viewed remotely (for security reasons). It could, however, be viewed by browsers running on the local server machine.

A more detailed message is available after disabling the default error message:

Server Error in '/' Application.
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Configuration Error 
Description: An error occurred during the processing of a configuration file required to service this request. Please review the specific error details below and modify your configuration file appropriately. 

Parser Error Message: Unrecognized configuration section 'httpCookies'

Source Error: 

Line 30:         <httpCookies httpOnlyCookies="true" />
 
Source File: c:\inetpub\wwwroot\Citrix\AccessPlatform\web.config    Line: 30 

In IIS Manager the CitrixWebInterface5.2.0AppPool is not created, and the Web Interface site is not configured with an Application Pool as expected e.g. XenApp Web Site.

If website is configured using a process from the RunOnceEx key, the following error may be seen:

Server Error in '/' Application.
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Configuration Error 
Description: An error occurred during the processing of a configuration file required to service this request. Please review the specific error details below and modify your configuration file appropriately. 

Parser Error Message: It is an error to use a section registered as allowDefinition='MachineToApplication' beyond application level.  This error can be caused by a virtual directory not being configured as an application in IIS.

Source Error: 

Line 44:         <authentication mode="Windows" />

Source File: c:\inetpub\wwwroot\citrix\accessplatform\web.config    Line: 44 

This is because the Default Web Site is not associated with ASP.Net 2.0. This can be seen from IIS Manager | Default Web Site | Properties | ASP.Net tab.

Before installing Web Interface, register ASP.Net 2.0 with IIS using the following command:

%windir%\Microsoft.NET\Framework\v2.0.50727\aspnet_regiis.exe -i

When performing an unattended install and configuring a website, either as a command line during the install or using sitemgr.exe, launching from the RunOnceEx key does not install successfully possibly because the HKEY_CURRENT_USER registry key is not loaded completely. This can be seen as the CitrixWebInterface5.2.0AppPool Application Pool is not created in IIS Manager, despite showing success in the logs, and the Web Interface site is not configured with an Application Pool as expected. Launching from the RunOnce key results in a successful install with the CitrixWebInterface5.2.0AppPool Application Pool created and assigned.

How to Disable the Default Error Message in Web Interface 3.0
http://support.citrix.com/article/CTX103673