When configuring multiple groups to subscribe to a single filter, and a user is a member of some of the groups, then the user will receive duplicated filter subscription email. Example of the configuration is as below:

From the screenshot, the user admin is a member of both of the group jira-administrators and jira-developers, and thus when JIRA sends out the filter subscription email, admin will receive duplicated filter email. And thus, JIRA should have the ability to send out email and keep track of emails sent to which users in order to avoid duplicated email being sent.