There appears to be a contradiction in the drowning of Noah’s son. The following verse says that Noah’s family was saved:
Noah, when he cried to Us, aforetime: We listened to his prayer and delivered him and his family from great distress. (21:76)
Another verse says that Noah’s son was drowned:
...And the waves came between them, and the son was among those overwhelmed in the flood. (11:42-3)
We know from the Qur’an that the Prophet Noah (sws) himself inquired from the Almighty about his drowned son even though he was promised that his family would be saved from the flood. In 11:46, he is told that his son is actually not from among his family:
He is no kinsman of yours: he is a totally un-righteous person. (11:46)
This negation is not a literal negation but negation in reality. An arrogant and a rebellious son of the Prophet (sws) in spite of being a son is in reality not a son after all. Consequently, he was not counted as being a member of Noah’s family by the Almighty, and the question of a contradiction, therefore, does not arise.