While editing an interface and even put in a ALIAS NetScaler just prompts with "Operation Not Permitted".

Run the alias command manually from NetScaler Command Line
set interface 1/1 -ifAlias TRUNK

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Problem Cause

In ns.logs it was observed that other parameters are also getting set while making changes to the inteface Alias from GUI.The parameter which was failing was the set ha monitor ON parameter.

Logs:
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ns.log.0:Sep 15 15:59:04 <local0.info> 127.0.0.2 09/15/2015:20:59:04 GMT NLR-A-NS01 0-PPE-0 : default GUI CMD_EXECUTED 139 0 : User nsroot - Remote_ip 10.1.1.6 - Command "set interface 0/1 -speed AUTO -duplex AUTO -flowControl OFF -autoneg ENABLED -haMonitor ON -mtu 1500 -tagall OFF -state ENABLED -lacpMode DISABLED -lagtype NODE -ifAlias MANAGEMENT -throughput 0 -linkRedundancy OFF -bandwidthHigh 0 -bandwidthNormal 0 -intftype "Hyper v" -ifnum 0/1 -lldpmode NONE -lrsetPriority 1024" - Status "ERROR: Operation not permitted"

This an expected behaviour as per Issue Id: TSK0312538
When VPX is installed on top of a hypervisor – the interfaces are registered based on what the hypervisors expose.
There will be several parameter given back to VPX when it tries to register - physical link state being one of them.
The way the drivers are written specific to each hypervisor is different – and in case of Hyper-V the physical link state information is not passed through the virtual interface, unlike Xenserver which passes on this information.
As a result since VPX does not have link state information in case of Hyper-V it will flag this information and on execution of the HAMON set command rejects as it does not apply in this scenario.