It seems that gems like alexandrites, precious jaspers etc. don't stack correctly when looted. If I had to guess what is wrong, I'd suggest that there are multiple loot with the same name but different id and therefore don't stack as expected.
How to reproduce:
Go to Tur Suil, farm the monsters extensively and observe that gems dropped might not stack but instead be placed in individual inventory slots.
How to reproduce:
Go to Tur Suil, farm the monsters extensively and observe that gems dropped might not stack but instead be placed in individual inventory slots.