The basic flaw is worse. They didn't just run one test, find the results they wanted and go with it. They ran a test with only an idea of what they wanted, then took all the results they got and picked out ones that were positive for conditions or treatments they could go with. It's like going into a test for a drug to treat heart attacks, finding that it doesn't do anything for heart attacks but does seem to lower cholesterol levels, and announcing that the trials of your new cholesterol medication were positive.
Having to declare up front what their goals are destroys the ability to cherry-pick like this. What we're seeing with the drop in positive results isn't so much the difference in clinical effectiveness of the drugs but the dragging into the spotlight of the pharma companies' ability to predict what their drugs will do and how well they'll do them. There's a very interesting blog here that covers a lot of this, and one conclusion that keeps coming up again and again is that medical biochemists and researchers don't really have a good way of predicting from lab results what a compound will do in a live human. It also highlights fairly often how the drug companies will keep pushing a drug through trials even though the results aren't encouraging. It's a common attitude in business and finance, that now that you've invested this much money in something you have to get some return out of it to justify the cost. It's also a common failing in gambling, the belief that now that you're in the hole you have to dig yourself out somehow. But in gambling, if you're holding a bad hand your best bet is to fold. Don't worry about how much you've already got in the pot, it's already lost. Fold and cut your losses before you throw any more money away. Drug companies are notoriously bad at making that decision to walk away. They're also notoriously bad at dealing with a field where there aren't many good rules you can follow to get results. MBAs like process and procedure and predictable results, and right now biochemical research is in a situation where the new stuff is all likely out in areas where there isn't a lot of research, there isn't a good map of the territory and you're going to be doing a lot of "poke it with a pointy stick and let's see what it does" work.