Once the dust settles from a new Jira install and you have users active in it on a daily basis, the little things start to get noticed. A frequent complaint is how Jira seems to spam users with email notifications. If you google around for "why am I getting duplicate jira notifications" you find alot of results, such as:
https://answers.atlassian.com/questions/44064/how-to-prevent-duplicated-outgoing-mail-on-notification to name a few of the best search returns.
Atlassian even put a wizard into Jira for admins to figure out why a specific user got a duplicate email on a specific issue and action. However, the wizard doesn't work for notifications that aren't about a specific action on a specific issue, for instance when someone uses the "Contact Administrators" form. Luckfully, duplicate emails are almost overwhelmingly not caused by bugs in Jira, but the way your user directory is setup and the way your notification schemes are setup. Doubly luckfully, here's the two rules that will help troubleshoot most duplicate email issues in my experience.
1) Jira, when it sends emails, only checks that the username is unique, not the email address.
2) Certain events get forwarded to everyone with the Jira Administrators global permission.
A messy user directory will make what looks like duplicate emails because of rule #1; if you have an internal directory with email@example.com as a username and you then connect Jira to active directory and importes domain\jsmith as a user, Jira will treat firstname.lastname@example.org and jsmith as two separate users (because they are!) even though they have the same smtp email address. If they are both in the same group that has a project role that gets notifications, it will appear that Jira is sending out duplicates when it's actually not.
For rule number two, let’s take the ContactAdministrators form for instance; it’s one of those system events that emails everyone with the Jira Administrator’s global permission. If you check your Global Permissions, you can see which user groups have the Jira Administrators permission. Then check the email addresses for everyone in every group with the Jira Administrator global permission; you will almost certainly find either duplicate email addresses (remember, Jira checks usernames for duplicity when it sends emails - not email addresses!) or unique email addresses that have the same destination (for instance, email@example.com and firstname.lastname@example.org may both be valid and go to the same person, depending how your email scheme was setup), or unique email addresses that result in a distribution group; perhaps you're email@example.com and you're a member of firstname.lastname@example.org. Jira will email both and not feel bad in the slightest.
Long term, you need to:
1) Be aware of Jira's behavior so you can be more tolerant of what looks like duplicate emails/spam.
2) Be very wary of internal directory accounts using the smtp email address of a distribution group. Jira will not parse the contents of a distribution group - you literally can't over SMTP.