PROBLEM DESCRIPTION:
Duplicate computers in the Sophos console

Attaching screenshots of the behavior:

This is a Sophos software known issue:

Issue: Duplicates of Sophos Central Servers in Dashboard
https://community.sophos.com/products/sophos-central/f/sophos-central/91490/issue-duplicates-of-sophos-central-servers-in-dashboard

Duplicate computers in enterprise console
https://community.sophos.com/products/endpoint-security-control/f/sophos-endpoint-software/8812/duplicate-computers-in-enterprise-console

Direct customer to software vendor support (Sophos support).

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Problem Cause

This is a Sophos software known issue:

Issue: Duplicates of Sophos Central Servers in Dashboard
https://community.sophos.com/products/sophos-central/f/sophos-central/91490/issue-duplicates-of-sophos-central-servers-in-dashboard

Duplicate computers in enterprise console
https://community.sophos.com/products/endpoint-security-control/f/sophos-endpoint-software/8812/duplicate-computers-in-enterprise-console

Customer allowed case closure.

Duplicates of Sophos Central Servers in Dashboard

Citrix App Layering recipe for Sophos Endpoint Protection 
http://www.jgspiers.com/citrix-app-layering-recipe-sophos-endpoint-protection/ 

Anti-Virus can be delivered in an application layer or the operating system layer, which one do you want to implement? 
Check the following guide for each method: 

Deploy anti-virus software 
https://docs.citrix.com/en-us/citrix-app-layering/4/layer/layer-antivirus-apps.html

Additionally here is the requested App Layering Best Practices guide: 

Citrix App Layering 4.x: Best Practices 
https://support.citrix.com/article/CTX225952