If you are seeing two comments for every JIRA update, you have two webhooks configured or you have installed the Atlassian Connect Aha! plugin as well as using the direct JIRA integration.
As long as the webhook run as user has product owner or contributor permissions to all products in Aha! that are integrating with JIRA, only a single webhook needs to be configured in JIRA. Many companies will choose to add an integration user to their Aha! account for this purpose.
If you are using the JIRA via Connect integration (rather than just the plain JIRA integration), then you should have no webhook at all. The JIRA via Connect integration has its own webhook that is not displayed in the JIRA web UI.
If you are using the plain JIRA integration as part of that installation, you will add the webhook to JIRA. If you also installed the Aha! plugin in your JIRA instance, you now have two webhooks because the plugin has the webhook.
You should remove the duplicate webhook or uninstall the Aha! plugin from JIRA. That will solve the duplicated comments. After the issue is resolved, duplicate comments can be removed as needed in Aha! by an Administrator.