No State is obligated to treat non-citizens as though they are citizens. There is no apartheid in treating non-citizens as non-citizens. Arab Palestinians are citizens of Palestine. Israel has, so far, declined to apply its (rightful claim to) sovereignty over the Arabs in Gaza and the "West Bank". Should Israel apply sovereignty over all of the territory, by definition, all non-citizens would become citizens of Israel. Until that happens there can be no claim of apartheid in Gaza and the "West Bank".
Within sovereign Israel, any claim of apartheid would have to demonstrate a system of two sets of laws based on something other than citizenship/non-citizenship, particularly ethnicity. I know of no such laws.