Did you pull up your activity on a web browser or just on the mobile app?  The mobile app does not show any segments that are hidden, so there is a chance you may have earned a CR on a hidden segment that you just can't see on the mobile app.  

On the web app. When I click on the link in the e-mail I arrive on this screen with the segment selected. It's not a CR and not a hidden segment:

If you post a link to the activity here, I can take a look and see what it looks like from my view.

Never mind.  I found the activity.  It does appear that the notification was a mistake of some kind.  Rather than two CR's, you had one CR and one PR.

Today I experienced the exact same behaviour again. One CR and one PR and e-mail says two CRs. 

Hey @transducer, 
Sorry for any trouble. Please submit a support ticket and include a link to the activity you are referring to as well as any screenshots of what you are seeing and our team can look into this.

What is the difference between a support ticket and this post? I tried to make a support ticket on https://support.strava.com/hc/en-us/requests/new and via the chatbot I came on this forum and created this question.

@transducer, 
Thanks for asking! The Community Hub & Strava Support are two different platforms. The Hub is great for general questions and information while our Support team will handle questions that require the member to share personal account information. We may also escalate to our Support team if a topic is highly complex or technical. I took a look and we are not showing any support tickets from your email. 

For the Strava instant answers (chatbot), if that cannot help with your inquiry, you will be directed to contact us by email. You should see the following:  

You can also reach out to support by emailing: support@strava.zendesk.com. Please be sure to include a link to the activity you are referring to as well as any screenshots of what you are seeing so our team can further investigate.

I hope this helps!