This is probably caused by subscribing to the article more than once. For example you comment on a question and subscribe. Then you answer the question and subscribe again. This will result in two subscriptions that each send you a notice when your answer is selected.
The ideal solution would be a deduplication algorithm that detects if the user is about to receive two e-mails of the same type. or just prevent hte user from subscribing multiple times.
That said this can be a very difficult problem to solve from a coding standpoint. I've spent days writing similar algorithms and days of work just to stop a few duplicate e-mails probably isn't worth it.