Hiya!
I can't help with this problem, I'm afraid, but wanted to put my head above the parapet too as it's also happening to me. Particularly frustrating as the peace of mind of having an up-to-date, accurate and low-maintenance 'in the cloud' back up of my photos was the main reason I shelled out for extra iCloud storage space and went through the whole rigamarole of setting everything up. In fact, my situation is probably even more straightforward. I've just the two devices - my MacBook Pro (mid-2012) and my iPhone 6. I back-up my iPhone to my MacBook manually so I'm fairly confident that auto back-ups can't be causing any kind of confusion.
I used iPhoto on my MacBook this morning to really simplify things for iCloud - spent ages deleting all my albums and loads of stuff I didn't need anymore, so now I just have my All Photos, Faces (which I don't need or use but still seems to want to be there front and centre in spite of my best efforts), Last Import and Videos - no bursts or albums or anything like that. So, all nice and tidy in iPhoto. A beautiful sight if I say so myself!
Checked my iPhone and everything's different - stuff I deleted still there, not clear what's on the iPhone itself and what's in the cloud etc. Just a big old mess. Logged into iCloud itself and that looks different again - deleted things still there, albums I never created popping up all over the place by date etc. So my 'syncing across devices' has just provided me with two different locations where I need to keep deleting, tidying up etc. Three if you include iCloud itself.
Anyway, I have a back-up of everything from before I started the odyssey of iCloud, so I'll just cancel it all and go back to hard copy back-ups - not a solution, I know, but I just can't dedicate the time to a cloud service that needs me to do everything three times. It's a bit needy.
All I've really wasted is the couple of quid I spent on extra storage which I'll cancel and a few hours of tidying things up on my MacBook Pro. This is by no means the end of my world but I am a bit disappointed, as I was under the impression that syncing across devices was what iCloud was meant to do. I thought it was peculiar when I synced Reminders and suddenly lists of reminders from months and months ago, long deleted, started popping up everywhere, the Contacts feature started cannibalising contacts from other accounts etc. All a bit 'iffy' in terms of where this long-deleted info is suddenly being pulled from (?!) and certainly incredibly messy. If we still have to go into iPhone, Macs, iPads and iCloud online separately to keep everything organised I'm not sure there's much point to it - in fact, for me at least, that's making work.