There's got to be a significant correlation between having the seasonal flu vaccine recommended for you, and being exposed to swine flu. Surely we should expect that people who choose to get seasonal flu shots do so in part because they're more likely than average to come down with the flu if they don't get a vaccine. Being at high risk for exposure to the flu is a clear mediating factor in leading to both getting every available flu shot and coming down with any strain that goes around that there isn't a vaccine for.
To put it another way, we vaccinate some people go keep them from spreading the flu. If there's a link between getting the vaccine and getting the flu if you don't get the vaccine, then we're vaccinating the right people, and we should go on vaccinating them. (But it's worth making sure people know that they can't act like they're immune to the flu this year.)
Of course, the study could have found an actual danger to the vaccine, but we can't tell until the peer review is complete; peer review is where people will come to some sort of consensus on what the risk is that this value should be compared to.