One possible explanation would be if you created a new Photos library on the MacBook and connected it to iCloud Photos at the same time that you enabled iCloud Photos on the iPhone. That would mean you have one Photos library with your old photos and another with the photos from the iPhone. You can check for this by quitting Photos on the Mac and relaunching it with the option key held down; see how many libraries are listed.
Another thing that could have caused a result similar to what you describe would be if you connected both the MacBook Photos and the iPhone Photos to iCloud Photos (which causes them to sync together) and then deleted on the iPhone the pictures that you didn't want on the iPhone (which would then delete them from the cloud and the MacBook). You could check for this by looking into the Recently Deleted album on either device (unless you also emptied that album).