Are there any flaws in using CTR as a metric?

Yes, there are some flaws in using CTR as a metric — the biggest con is that CTR doesn't account for user intent. If you wish to increase your conversion rate, you must know what actions users take on your site or landing page and how they relate to the user's intention. So, you can adjust your strategy based on this analysis.

The best way to identify user intent is to ask the users themselves. However, if you don't have the time or resources to do so, you might have difficulty figuring out where to put your efforts.