Even with sampling bias, we could still be seeing something legitimately weird. We expect to detect some certain number of exo-planets with a certain range of characteristics with our current technology. We don't think this set of exo-planets is necessarily representative of the average exo-planet in the galaxy, because of the limits of our technology, but we expect to look at X stars, and see Y planets, which look about like Z (where Z is probably Jupiter-sized planets orbiting at Jupiter-like distances). We might also expect to see a few weird planets, where the solar systems are aberrations or we just got lucky and detected something better than we'd expect with our technology.
But what this article seems to be saying (maybe a little poorly) is that the set of planets observed is not the subset of planets we expected to observe. We expected (say) to look at 100,000 stars, see 100 normal Jupiters, fail to see 9,900 other normal Jupiters that were there but we didn't detect, and see 1 aberration, like an Earth-like planet we accidentally detected or a hot Jupiter representing a weirdly captured wandering planet. Instead, we saw 1000 aberrations, hot Jupiters. More than we expected to see based on how we thought solar systems formed.
Just because the unexpected thing is actually extremely easy to detect once you're looking at the universe in the right way doesn't make it any less unexpected. Even if we eventually find millions more solar systems that look like ours than ones with hot Jupiters, we might still have to figure out why there are so many more hot Jupiters than we expected.