I'll just list three quotes that bugged me:
> The X, H, R(k), M and SWAP gates are discussed in detail and results show linear scaling as the number of qubits are increased.
How did they manage to spend linear time per operation when you can't even make two qubits interact with the given operations? Just working on the qubits individually will be constant time instead of linear time.
> The efficiency is still unresolved for these coherent control gates. The number of edges can still grow exponentially for coherent control gates, however, it remains to be seen if duplicate edges can be efficiently merged.
They didn't do the hard part yet, but the easy part was easy, so they expect the hard part to be easy.
> if BPP = BQP then it is possible that quantum mechanics can be de-randomized by a deterministic theory thus confirming Einstein’s conviction that nature does not play dice
Confusing "can be simulated classically in polynomial time" with "is not random". The existence of merge sort doesn't prove that quick sort isn't using randomness.
The arguments for randomness in quantum mechanics aren't based on complexity in the first place (e.g. we can trivially simulate Bell tests).