I think the dupes exist in both notifications and your actual stream. They are created any time someone comments on a photo in an album. It spawns an entirely new post on that photo in your stream. So if you have a popular stream and people go to an individual photo in that album and comment on it, it auto generates an entirely new post for that photo in your G+ stream. There should be an option to disable this at least.
I think photo organization is the weakest link in the G+ Photos experience.
At flickr, for example, if I want a photo to be in my album of San Francisco photos and San Francisco graffiti album and graffiti album I can have it in all three. If it gets more than 25 faves I can also even have it in my 25 faves or more album. http://goo.gl/FrgrY
As an added bonus I can create albums of albums. These are called collections. So I can have a collection of photos dedicated to my project of documenting the 100 largest American Cities specifically. http://goo.gl/3FMH
All of this great organization without dupes in my flickrstream, without having to make multiple copies of the same photo, and almost entirely automated by keyword. I push one button every day and it auto updates over 1,700 albums. Automation rocks.
At Google I literally have to make three separate copies of the exact same photo and manually
put it in each album, which then will spawn 3 duplicate undesired entries (if comments are made on a photo in any of the three albums) to my stream making an absolute mess. Even if you delete the dupe photo that has been spawned without your desire it will just create an entirely new
spawn the next time someone else comments on it. It would be like playing whack a mole to try and kill all the dupes that are spawned by this auto post generation nuisance.
There are lots of reasons why you dont' want dupes of the same photo in your stream. It's confusing to followers who may have already seen a photo 2 days ago to see it pop up new again. As a consumer of photography when you see someone flooding your stream with 50 photos of the same event all at once you interact less with any individual photo. You also might unfollow the person for spamming your stream. I might want to see one or two photos of your best photos from your family vacation, but I don't want to see 50 when your 14 year old niece posts Awesome
on all 50 of them.
Also it makes finding the photo later and comments tied to it difficult. If I want to follow comments on the group shot that I took of a photowalk and it exists two places in my stream it's harder to follow the 2 entirely different threads dedicated to it. Consolidating the conversation on a single photo makes more sense.