In a nutshell, we know that science more or less progresses from one theory to another after the existing theory has been falsified (Popper), but this transition does not happen overnight, even after a falsifying result has been put forth. That is because science is really structured with a "hard core" hypothesis (say, in physics, that nothing moves faster than c), and various "auxiliary hypotheses" that bear the brunt of criticism before the core belief is attacked (say those that posit the integrity of the measurement instrument, for example). And that is all that is going on here. There are many, many theories that are going to be dismantled before physics transitions to something post-relativity. It's just the way the assumptions are structured.
While this may seem trivial, we see this playing out in the battle of classical against behavioral economics. Are the results of experimental psychology admissible in the criticism of certain economic models? Models don't claim to be perfect, after all...
1. http://en.wikipedia.org/wiki/Imre_Lakatos#Research_programme...