Let's say you have an article that has comments inside the article as well as in a forum topic. Each time someone posts a reply/comment, both the topic and the article show up on the activity stream.

I believe these are the same thing so on the activity stream, it should only display one item. The system knows both are connected and could only display one of them.

In the stream's settings, have you looked at "Show me" settings:

• Content items, comments, and reviews
• Content items only

I have. This setting just limits the number of items to one per topic, if more replies were made in that topic.

It still shows article and topic for comments as two separate items though.

I have to correct myself. The duplicate content is only visible when the article is created. In that case the stream tells you a new article and new topic have been created but they are the same.

After you make new comments (even if you comment on the article) they are only shown once as new topic replies.