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Often, in science, when we have evidence that doesn't fit our paradigm, we bend it until the paradigm collapses.
Although there is plenty of decent evidence for evolution, is there anything that does not fit the evolutionary paradigm? Is there any biological evidence that is not suggestive of or seems to disprove evolution? Or is everything merely hunky-dorey?
Evolution is a broad field of knowledge. There are definitely a few elements of our current theory of evolution that does not perfectly match observations. However, those concern small details and might not of much interest to you. Here are a few examples
We don't know the relative importance of background selection and selective sweep at explaining genome-wide variation in genetic diversity.
We don't really have much of an idea what fraction of speciation happen in sympatry.
We don't understand well how recombination rate evolves to differ in different genders.
We don't really understand what are the limits and/or costs of phenotypic plasticity that makes phenotypic plasticity less frequent that we would otherwise expect.
We don't really understand the patterns of genetic diversity on sexual chromosomes at the intersection with the pseudo-autosomal region (PAR).
We don't fully understand how much expansion load (a type of mutation load caused by the sampling of individuals at the expansion edge of a population) there is in human population.
We don't really know whether the mitochondrion (and other double membranes organelles) was first a endo-parasite or a endo-symbiont.
If you are asking whether there are evidences suggesting that evolution is not happening or that humans and chimpanzee do not actually share a common ancestor but were created independently, then no, there is no such evidence.
You should have a look at the related post Is Evolution a fact?
I agree with Remi.b that there are some things we don't yet fully understand. However, Darwin got it right. A theory is an explanation of observations. It is laid out to be disproven. Evolution, as a theory, has stood 158 years of attack without being disproven. It predicted Mendelian genetics, and molecular biology. Sexual selection seems to be outside natural selection, which is why Darwin considered it a special kind of selection. The "theory" is as strong as science can ever support. "Facts" and "proofs" are for math. But if we had any proof that evolution did not fit our observations, the theory would be falsified.
Please clarify your question. Evolution per se is an observation, not a theory. We see it literally every day (I am a virologist and my organisms literally evolve on that time scale). It is impossible to argue rationally that evolution doesn't occur; it's like denying that when I spill my coffee the mess falls downward. Even pre-Darwin scientists universally accepted that evolution occurred. Even "Creation Scientists" (who are not scientists, but religious fundamentalists) can't deny that evolution occurs. Evolution is a fact, not a theory.
Are you asking if the theory of evolution through natural selection (which is what most people think "the theory of evolution" is, and what religious people call "Darwinism") explains everything? No, of course not. It's a theory that is over 150 years old, and it hasn't been the sole theory underlying evolution for over 50 years. Other theories, including sexual selection, neutral drift, and nearly-neutral drift, were proposed in order to account for many aspects of observed evolution that natural selection doesn't account for.
If there were other aspects of observed evolution that weren't accounted for by one or more of these underlying theories, then further theories would be proposed. Evolutionary theory is pragmatic, not dogmatic.
At the moment, there are no observations I'm aware of that can't be accounted for by the present combination of theories.
