Lucrezia Borgia, upon being told that Prince Djem died of malaria, states that he was killed by a mosquito, but it wouldn't be discovered that the disease is transmitted by mosquitoes until the 19th century. The name "malaria" literally means "bad air", and it was this bad air in swamps that was believed to cause the disease.
Lucrezia, while being fitted for her betrothal dress suggests that a wedding gown ought to be white. However, white did not become a popular option for wedding dresses until 1840, after the marriage of Queen Victoria.
Prince Djem was in his thirties when Rodrigo Borgia became Pope, and died two years after Lucrezia's wedding while in French captivity.
In reality, Prince Djem was put under custody of the Papacy in 1489, 3 years before the election of Alexander VI.
In the 1490s the Ottoman Empire had just come out of a long, fruitless war against Egypt for control of Syria and eastern Anatolia. It wouldn't control anything near Persia until the Battle of Chaldiran in 1514.