I also got intrigued by this problem while listening to prof.Vazirani lectures on Quantum Computing.
I kind of explained to myself this "contradiction" by saying that you can "copy" the base states $|0\rangle$, $|1\rangle$, $|00\rangle$, $|11\rangle$, etc... but you cannot copy their amplitudes if they are in a superposition.
Therefore the no cloning theorem says that you cannot copy $|\psi\rangle = \alpha|0\rangle + \beta|1\rangle$ to another qubit that is now in the state $|\phi\rangle = |0\rangle$ BUT if $|\psi\rangle = |1\rangle$ you can make it became $|\psi\rangle = |0\rangle$ for instance.
Also, I think that when doing quantum computations, you are interested in the end if your Qubit is in the state $|0\rangle$ or $|1\rangle$ not in the amplitudes associated with the base states when in a superposition.
Any comments on this answer will be greatly appreciated, since I'm trying to teach myself Quantum Computing and sometimes I get stuck in some concept like this one.