They do not contradict each other... 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 when you mentioned that the first verse tells us that 'having' a son is impossible for God without a consort. But, I have to tell you that 'choosing' a son is not impossible without a consort.
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 to differentiate the two verses.
The two verses compliment each other and as you said it, "these are 2 separate verses discussing a topic" i.e. God is one.
WALLAHUA'LAM...