Steps to replicate:

1. Set up a JIRA Service Desk with incoming email configured
2. Email the email address set up in step 1
3. Reply to the email created in step 2 (making sure the email address from step 1 is in the "to:" list)

Result:

Two JIRA issues are created

Expected Result:

One JIRA issue is created from the email sent in step 2, and then a comment is added to that ticket from the email sent in step 3. This is the behaviour that JIRA Core currently demonstrates.