Would verify that the user(s) have configured their notifications to receive emails correctly. If this issue pertains to followed content notifications, please keep in mind that if you follow a category, you will not get reply notifications to content items by design. You need to also follow the content item.
For example, if you follow a forum, you would need to also follow the topic in order to receive notifications about replies in that topic.
If all the above is configured correctly, we would require an example user's display name, the type of notification they aren't receiving, and if a follow content notification, the content item URL they are expecting to receive a notification but are not.