Also, there is a TLS port (5053) and non-TLS port (5050) configured for IQService and it was never a problem before while executing native scripts.
But, everything works well when the native script is detached from the AD source settings and not sure what causes the ScriptExecutor service stopped. When I checked the services at the time I got the error, I see the service was up and running.
I disabled the non-TLS port (updated the port number from 5050 to 0) in IQService and the scripts are now called.
Why is necessary to be removed? And I see the IQService was updated recently, is the latest version enforced to be communicated only with TLS port, else services are temporarily stopped?