Shared photo library moving into new photos app?
If you have Photostream turned on and set it to download Photostream photos, then iPhoto will put them in an Event by month. It will look similar to other photo Events that you've created. iCloud Photo Library sees these as just normal photos and will upload them. Everything in the System Library (which means the default Photos library) will get uploaded, so the only way to stop it is to turn off iCloud Photo Library or put those photos into a separate Photos library.

If you have iCloud Photo Library turned on in your Mac and iPhone, then they will eventually sync up.

All pictures in your iPhone Photos app will get uploaded into iCloud Photo Library (including screenshots and saved photos from other apps/internet).