Stop-WebAppPool does not stop pool, at the same time I can stop it in IIS panel

I'm using poweshell remoting to restart application pool during deployment.

Before delpoyment site is switched to offline mode using app_offline.html.

Also I deploy temporarary web.config to prevent early restarts:

<?xml version="1.0" encoding="utf-8"?>

<configuration>
    <appSettings>
        <add key="Environment" value="development" />
        <add key="Deployment" value="true" />
    </appSettings>
    <system.web>
        <httpRuntime waitChangeNotification="300" maxWaitChangeNotification="300" />
        <!-- <customErrors defaultRedirect="app_offline.htm" mode="On"/> -->
    </system.web>
    <system.webServer>
        <modules runAllManagedModulesForAllRequests="true" />
    </system.webServer>
</configuration>

Then webdeploy installs new version.

The powershell remote commands are executed Stop-WebAppPool -Name $poolName/Start-WebAppPool -Name $poolName.

Then I deploy full web.config and remove app_offline.html.

The problem is that Stop-WebAppPool does not stop pool, it stays forever in Stopping state (according to powershell Get-WebAppPoolState). At the same time I can go to IIS panel and do stop pool manually without any problems. There is single pool, single machine, so everything is correct. Somehow webdeploy and app_offline.html breaks powershell commands, I tested restart script separately it works as expected.

Relevant thread: https://help.octopus.com/t/issues-stopping-app-pools-during-deploy-when-autostart-being-used/20837