Because the script says it was dipped in ketchup.
No rly, most cling to the colours in the original game. I don't know the colour schemes in Crisis Core, but I think they are similar or even the same.
Though even in FFVII there were inconsistencies. Sometimes a yellow materia on the map would look purple, and so on. But usually the colour was correct.
I like the fact the materia is a different color because it proves how omnipotent it is or can be.
EDIT: Ahh, damnit not again!!!