The story of Moses confrontation with the Pharaoh of Egypt is a very prominent one in the Quran. It is told in nearly a dozen places, see this list. This story being retold so often, and its details being scattered in so many places, calls for comparing the different versions and discovering similarities and differences between the different versions of the story in the Qur'an as well as the similarities and differences between (the various versions of) the Qur'an and the Bible.
In Exodus 1:8 - 2:10 and Sura 28:1-13 we find the story of the birth of Moses. These two texts have plenty of differences and disagreements. However, the Qur'an agrees with the Bible that Moses was born at a time when the Pharaoh of Egypt had given the order to kill all male infants of the Israelites; only female babies were allowed to live. The Bible gives a clear reason for this cruel decision of the Pharaoh (Exodus 1), while the Qur'an does not tell us why this command was given, except for calling Pharaoh a proud and evil man:
Verily, Fir'aun (Pharaoh) exalted himself in the land and made its people sects, weakening (oppressing) a group (i.e. Children of Israel) among them, killing their sons, and letting their females live. Verily, he was of the Mufsidun (i.e. those who commit great sins and crimes, oppressors, tyrants, etc.). S. 28:4 Al-Hilali & Khan
The Bible and the Qur'an agree that Moses was miraculously saved from this fate and grew up at the court of the Pharaoh. Later he killed a man (who had oppressed the Israelites) and had to flee from Egypt and lived in Midian. When Moses was an old man God spoke to Moses from within a burning bush. Moses was called to be God's messenger and was sent back to his people and to Pharaoh. Pharaoh didn't believe Moses and didn't obey God's message. There was then a confrontation between Moses and the Egyptian magicians in which the miracles of Moses proved to be more powerful than those of the sorcerers.
Then the Qur'an departs from the Biblical story in a major way. After the showdown of Moses against the sorcerers of Egypt in which the miracles of Moses are so convincing that the sorcerers afterwards believe in the God of Moses, and Pharaoh therefore punishing them for their betrayal (S. 7:113-126), we read again that Pharaoh gives the order to kill the male infants of the Israelites:
The chiefs of Fir'aun's (Pharaoh) people said: "Will you leave Musa (Moses) and his people to spread mischief in the land, and to abandon you and your gods?" He said: "We will kill their sons, and let live their women, and we have indeed irresistible power over them." S. 7:127 Al-Hilali & Khan
And indeed We sent Musa (Moses) with Our Ayat (proofs, evidences, verses, lessons, signs, revelations, etc.), and a manifest authority, To Fir'aun (Pharaoh), Haman and Qarun (Korah), but they called (him): "A sorcerer, a liar!" Then, when he brought them the Truth from Us, they said: "Kill the sons of those who believe with him and let their women live", but the plots of disbelievers are nothing but errors! S. 40:23-25 Al-Hilali & Khan
The Qur'an mentions the slaying of Israelite boys in these passages: al-Baqara 2:49, al-A`raf 7:127,141, Ibrahim 14:6, al-Qasas 28:4, Ghafir 40:25. Among those, S. 28:4 refers to the slaying around the time of Moses' birth, S. 7:127 and 40:23-25 speak of an alleged second slaying after Moses had come back as a prophet, while S. 2:49, 7:141, and 14:6 look back at the fact that the Israelite boys had been slain, but it is unclear whether these verses refer to the first or the second slaying period, or even both.
On the level of facts, this is in blatant contradiction to the Bible. There was no second slaying of Israelite boys several decades after the birth of Moses, after Moses had come to Pharaoh as a messenger from God. The author of the Qur'an was apparently quite confused about this matter.
The author's confusion can also be seen from the fact that the story of the Qur'an is incomplete and incoherent in both instances, when it recounts the Biblical story of the slaying of Israelite baby boys at 