Off the top of my head:
1 in Cyseal Inn murder scene
1 from Evelyn in Cyseal
1 from Blood Cove's pirate boss
2 from Immaculate basement in Silverglen
1 from Immaculate trials
1 from Goblin Village talking totem
1 from Maradino's secret lair
1 from the altar in the hidden Immaculate temple
1 from Hiberheim Prison's talking iron maiden
1 from Phantom Forest, the statue behind Cassandra's grave
1 from Knight's Tomb, from the sarcophagus itself
I'm sure there are more, but those are what I can remember immediately.
I got all those yet still in same position as the original poster in that have firstly an inactive portal, secondly the forbidden zone one which I think isn't supposed to be unlockable and thirdly the first garden one...all three I don't have access to but the main problem is source temple door fails to open despite I think had more than enough stones. I found loads more too so I think the game is just glitched and some people like myself have hit dead end after spending over 50-70 hours playing...
I found a way around the problem though by using throwing of teleport stones past source temple door but I wonder if bypassing it is going to cause yet more problems with things breaking more.
What would be nice is if there was a stat tracking function in the character profile to show how many have already among other stats or even a console command function where we can reset AI and other stuff. I wonder if there is any way to open and read the savegame file in readable format to check what it has recorded that I have already obtained.
I wonder if mine is not progressing or recognizing that I should have enough stones already because this guy is glitched in the homestead...
Or maybe one of these glitches I have caused the games to no longer record or records the quantity of stones I have found
(spoiler alert).
I killed Loic as he ran away so that quest is now glitched I think and Lawrence was killed too as part of another quest so that one is also bugged.