So yes, there is a well understood process for invalidating patents. And that is, no doubt, going to play a major role in the case. But all that comes after the problem itself--the injunction lasts while people are showing prior art and forwarding any other arguments they have.
So my complete understanding is as follows: the fundamental problem here is the patent system. The issue is that Apple was able to get weak patents and then is able to use those patents to get an injunction on a product before the patents can get tested in court. This lets them leverage a weak hand and ~$100m to weaken their competition, regardless of the patents' actual validity. This, combined with a bunch of other problems with the patent system (oh, let's patent math as long as it's run on some computer!) is why there is a call for patent reform. The reason people are annoyed with Apple is that, instead of being nice, they're abusing a broken system to damage their competition.
Of course, I'm certainly no lawyer and have been following this case only superficially. This is a good summary of what I think is going on, but could have no bearing on reality whatsoever.