If user subscribe topic and check options "Someone replies to a topic to which you are subscribed" and "Someone quotes you in a post" in notification setting and someone else quote the first user he/she will get two notifications about the same post.

I think it's linked to this issue (https://tracker.phpbb.com/browse/PHPBB3-13811) - if I disable and save "Someone replies to a topic to which you are subscribed" notification and enable it again I don't have this issue (even if I disable emails again).