It seems like cutting corners to save time and money is what has lead to this, and that shouldn't be a surprise to anybody. Something of this scope and importance shouldn't be treated in the manner that Bechtel and the DoE initially did. I guess the issue becomes, what is the flow rate of all these things, and how much water is accumulating on a daily/weekly basis? If it's some marginal amount, then yes it's still a problem, but one that can be fixed given time.
Water treatment is such a huge issue with energy, and I don't think it's one that people think about that often. The two biggest culprits are probably Nuclear Energy, and the Hydrofracking process.