Disagreements are one of the things which are often mistaken for legitimate “controversies” by cdesign vermin, perhaps intentionally or simply because they do not take the arguments in context. The assumption here is that all disputes about specific aspects of a theory or hypothesis are akin to disputes about the theory or hypothesis. A good example of this would be the manufactured “controversy” about the definition of a species. The biological species definition, cohesion species, typological species, or any of the other dozen or so “species definitions” are all useful in certain situations. The discussion isn’t about some intrinsic characteristic in an organism, the disagreement is purely fabricated for our own purposes. How we classify organisms is pretty much of no relevance to the phylogeny of an organism for purposes of understanding the evolutionary history of the organism. The entire basis of the “one species doesn’t become another species” argument stems out of the misunderstanding of how we define a species, not intrinsic properties of a population.
For example, if we have three populations, one of which can (and does) interbreed successfully with both, while the other two are not capable of hybridizing (such as present in some ring species complexes), we are left with the issue of how to distinguish one from the other. Two species clearly exist according to many species concepts, yet the existence of the first population which can interbreed with both populations prevents any obvious means by which to classify them.
This sort of difficulty in classifying organisms and debate of which species model works best in various situations is considered to be a “controversy” in evolution. Note what isn’t controversial: organisms evolve, populations of organisms become isolated, populations of organisms evolve separately and distinctly owing to the unpredictable nature of genetic drift, and so forth. The only legitimate arguing point is “how do we define THIS group of organisms for purposes of specificity?” Using subspecies names is only partially effective at this since two populations are distinct enough to merit their own species name. Should the first population be elevated to species status from both others even though it can hybridize?
In short, when you hear about “controversial” issues in science, be sure you look at what IS controversial, but also look at what parts are not. Context is everything.