According to some the theory of evolution has experienced something similar.
-_- according to who, and what was experienced? Fossils have been documented for thousands of years by humans, even if people didn't make many connections between them and modern organisms until much, much later. We've born witness to changes in the traits of populations and have even used it to our advantage.
The same with evolution. It is assumed that all changes in life have evolved through natural selection and when there are anomalies another idea is devised to explain things ie Darwin said there should be gradual and continuous transitions but we find there are many gaps so the idea of Punctuated equilibrium was devised.
-_- and when atomic theory was new, the model for the atom was just a tiny sphere. As our understanding of the world expands, theories become more detailed and represent reality better. Of course Darwin's version of the theory of evolution would be different than the modern one, he didn't even know about DNA and mutation! Punctuated equilibrium, by the way, is not a consequence of, say, gaps in the fossil record, as many people seem to think it is. That may have inspired the initial idea, but gaps in the fossil record are not evidence for it and are not the reason it took off. Rather, it is a product of there being notable differences between organisms in the fossil record despite some relatively small time frames between some of them, combined with periods of less change also observed in the fossil record. Trilobites, which have a remarkably complete fossil record, were used to demonstrate punctuated equilibrium. Punctuated equilibrium actually requires more complete fossil records to properly demonstrate evidence which is distinguishable from gradualism, since gaps can easily be explained by "the intermediates simply haven't been found yet or unfortunately didn't fossilize". Plus, it is not as if punctuated equilibrium means gradual change doesn't occur. Rather, that gradual change isn't the only way.
Or when distantly related creatures are similar the idea of convergent evolution explained this.
-_- the DNA of organisms for which convergent evolution applies is too dissimilar for their lineages to be shared recently enough to explain the superficial similarities, and their physiology is similarly dissimilar when evaluated in detail Marsupial moles and eutherian moles visually look very similar, but their physiology is noticeably different.
marsupial mole skeleton:
https://pbs.twimg.com/media/CyoTJcLUQAIgeCK.jpg
eutherian mole skeleton:
https://farm8.static.flickr.com/7298/27057689530_44a00135ff_b.jpg
Look at how much more elongated the eutherian mole skull is compared to the marsupial mole. Look at the difference in the thickness and shape of the bones in the tails. Look at those large front teeth the eutherian mole has but the marsupial mole has no similarly sized front teeth. This is convergent evolution: looks similar and has a similar niche, but structure is more different that outward appearances would cause you to expect.
Yet some scientists say that natural selection is not a dominant force in how life changes and there are other non-adaptive forces more responsible that can explain better why there are gaps in the fossil records and why distantly related creatures have similarities.
Sure, some people think that genetic drift and other factors, which are a part of the theory of evolution, contribute more to how organisms change over time than natural selection does. Not particularly popular stances, but yeah, they exist. It's not as if people claim that the theory of evolution is inerrant and incapable of being improved, so why does it matter? I guess Christians never disagree on scripture OH WAIT THEY DO.
The fossil record is not the best evidence for evolution BECAUSE it is impossible for every species which has ever lived to end up being represented in it. Fossils are rare and the conditions necessary to produce and maintain them are very specific. Certain organisms fossilize better than others, which is why there are more trilobite fossils than, say, jellyfish fossils.
By the way, similar =/= the same. Similar adaptations are easily explained by evolution; for example, it makes sense for aquatic organisms to have body shapes which produce less drag in the water, hence the similar shape of sharks and dolphins. The internal structure of these organisms, however, is very different. Flight has evolved in 4 independent lineages, but it was different each time. The same abilities can evolve independently, but they won't evolve in the same way or originate the same way.
Maybe the assumptions for some of the long-standing ideas are wrong and need revising.
Pfft, you bring up punctuated equilibrium as if that whole situation didn't take place long before I was born (my mother was 1 year old when the idea began to take off in 1972).
Heck, it's brought up in my text books as a legitimate thing, so what "correction" are you looking for?