Submission of bad papers, even the publishing of bad papers is certain to happen. Since the whole enterprise is dependant on humans cross checking one another it will not be uncommon for faulty research to go unchallenged for some good amount of time. Others will need to be chasing that same research in order to cross check the one who makes the claim, that requires interest in the field and careful experimentation.No one claims that science was ever free of misconduct or bad research. Indeed, the scientific method itself is intended to overcome mistakes and misdeeds. When scientists make a new discovery, others review the research skeptically before it is published. And once it is, the scientific community can try to replicate the results to see if they hold up.
Science is a messy business because it is a human pursuit. That is why scientists are not to be trusted on their word. After all, they are just human, like any of us. Things can be exascerbated by the pressure to succeed, the competition for grant money, especially considering the small amount of dollars available in curiosity driven research. If there is no "Ipod" at the end of some experiment, it can be quite difficult to get the funding necessary.
But what we see in this article is an example of humans not following the strict discipline necessary for good science. In a perfect world people would not be tempted to ignore what their data tells them in order to affirm their pre-conceived bias. But this is not a perfect world, and that is precisely why we need peer review. To put the claims of others to the test and to see if what they say about the world is true.
Frauds will always be with us. Simple mistakes will always haunt our best efforts. These will only ever be exposed by scientific cross-reference and fact checking. We call that peer review. Our current process isn't the best there could be. There is always room for improvment, and nobody ever claimed that scientists are perfect and that is the purpose of this system.
As in history, there is a tendancy to hero worship. Scientists may be trusted, even if they advocate smoking to increase health as they did in the past, simply because somebody has called them a scientist. But there are no magic words, and simply calling someone a scientist does not imbue them with the mental riggor, and honest determination necessary to confront their deeply held, or fervently wished for biases.
The health and vitality of our scientific processes are dependant on the people who perform them and you can't blame the scientific process on these bad papers any more than you can accuse a car of being a lemon after filling the tank with sand.