Technically, you are right, with Arabia, the Ottomans and Mali, but let's not forget that the game also includes pre-Islam Nubia, Persia, Egypt, Indonesia...
Sorry but the argument that there are a many "civs from countries which are muslim today but there werent back in the day" as an argument against adding more actual Islamic civilizations is much more od the infamous "technical" variety of truth than just admitting there are only three muslim civs in the game
Ancient Egypt is, in every aspect, completely and utterly separate entity from Islamic Egypt so it obviously doesn't count to the counter of Islamic civs. The only things which connect ancient Egypt and Islamic Egypt are some meager linguistic remnants and genes. (Thats actually an irritating problem for me in video games - we are never going to get Islamic Egypt of Fatimids, Ayyubids and Mamluks because somehow that completely alien entity of ancient Egypt, whcih they couldn't even decipher writing of and knew nothing of its history, somehow it covers Egypt of Cairo, Saladin and Copts)
Persia in civ series is always depicted as 100% Achaemenid zoroastrian entity so it also doesn't count as "Islamic civ". There is of course cultural continuity from Achaemenids to medieval Iran, but unless I see a single tiniest bit of civ's design of Iran mentioning its Islamic part then I don't count those beings as Islamic.
Pre - Islamic Nubia is very different entity even from Christian millenium of Nubia, not to even mention Funj which came like a millenium and few centuries later.
Indonesia is a weird case, its greatest centuries came under Hindu-Buddhist dynasties so it usually gets this treatment, here actually I have no problems with that at all, but it still doesn't count as "technically" Islamic civ.
There are three Islamic civs out of 50 in this game (if we get no more), Arabia, Mali and Ottomans. I'm Iot saying there should be some idiotic quota for cultures, Religionz and regions, it was just my personal offhand disapointment, but I think saying there are much more Islamic civs that this because "they fit modern borders..." is much more "technically true" statement than "actually true" one