They do not contradict each other... the point is: no matter how, God has no son.
first, the verses...
6:101 Wonderful Originator of the heavens and the earth; How can He have a son when He has no consort? He created all things, and He hath full knowledge of all things.
39:4 If Allah had willed to choose a son, He could have chosen what He would of that which He hath created. Be He Glorified! He is Allah, the One, the Absolute.
The first verse Allah uses the word 'have a son' - meaning having a son of His own genetically. Refer the meaning of the word 'have' with regard to baby here http://dictionary.cambridge.org/define. ... &dict=CALD
You were right if u tell us that 'having' a son is impossible for God without a consort. But, I have to tell you that 'choosing' a son is still possible without the second verse.
The second verse uses the word 'choose a son' meaning - selecting from what is already existed. Refer the meaning of 'choose' here http://dictionary.cambridge.org/define. ... &dict=CALD
Why didn't He repeat the word 'have a son' in the second verse? If the second verse uses the word 'have' e.g. "If Allah had willed to have a son..." then there is a contradiction.
But Allah is Allknowing, He uses the word 'choose' or 'take' a son and not 'have' a son in the second verse to differentiate the two verses. The two verses compliment each other. WALLAHUA'LAM...