I'm not sure when this started as I haven't noticed until now. I religiously go and re-edit photos, add keywords, locations, etc. and thought it would replace the existing photo on Flickr, now it's uploading completely new copies and now I have quite a few duplicates in my photostream.
Example, If I have a photo I uploaded 6 months ago and I go in LR, make any change, it marks it for re-publishing. Now it duplicates it and uploads a new image.
Please do Help > System Info and report the exact version of LR and Windows or Mac.
Windows 7 and I'm using LR 2015.3 (the most recent update at this time that brought back the old Import dialogue)
I will say that I skipped the previous update 2015.2, I assume.
Please file a bug report on the official Adobe feedback forum: Recently active topics in Photoshop Family about Photoshop Lightroom. The more details you provide, the more likely Adobe might pay attention. (This forum here is primarily a user-to-user forum in which Adobe product developers rarely participate.)