Mostly, what they don't have the wit to ask. Here's an example.
I thought I wrote something about this New York Times article on a possible explanation for colony collapse disorder, which is killing bees. But apparently I didn't.
A group of scientists led by Jerry Bromenshenk of the University of Montana in Missoula, along with some Army scientists, found both a fungus and a virus in dead bees, leading to the suspicion that the combination of the two is the cause of colony collapse. The article is a bit better than the average science article of this type, because it does qualify the finding a bit, although someone skimming the article might well conclude that the cause of colony collapse disorder had been found.
But it turns out that Bromenshenk has a grant from Bayer AG, the manufacturer of pesticides that might be associated with colony collapse disorder. And that funding just happened to come at a time when Bromenshenk had signed on to serve as an expert witness for beekeepers who brought a class-action lawsuit against Bayer. Bromenshenk also has a company of his own that might profit from finding that disease, not pesticides, are the cause of colony collapse disorder. The Times reporter, Kirk Johnson, appears to have expected Bromenshenk to have told him these things.
Scientists can be horrendously naive about conflicts of interest. To some degree, their naivete is justified: they manage to do good work anyway, and Bromenshenk's findings may well stand up.
In an ideal world, the funding would come from sources that don't have something to prove. That would mainly be the government. But some long time ago, we became convinced as a society that funding from private companies, and assigning intellectual property to them, would be a good thing for the universities. So situations like Bromenshenk's become more likely. Yes, the university's administration should be watching for conflicts of interest, and so should the scientists. But, as I say, scientists are famously naive about such things, and, unfortunately, the prospect of funding tends to blind the administration.
And, um, reporters are supposed to be watchdogs, too, but I guess they may well have bought into the idea that the conflicts of interest involved in industry funding of research are purely illusory. Not even worth thinking about.