In his book The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution, Carroll discusses the use of genetic markers such as LINEs and SINEs (long and short interspersed elements, respectively) to reconstruct evolutionary relationships. He concludes:
biologists have sufficient forensic evidence to determine species' kinship beyond any doubt. 
Similarly, Myers derives similar certainty from the fossil evidence:
The evolution of whales is also a matter of fact and evidence. We have the fossils; we can see a pattern of change across geological time, from those hooved terrestrial quadrupeds to flippered ambush predators adapted to living in the shallows to four-flippered, paddle-tailed swimmers to obligate water-dwellers with flukes and no hind limbs, with many stages in between. It is a beautiful and strongly-supported example of macroevolutionary change. So yes, we believe it — you'd have to be blind to ignore the testimony of the rocks.
Fallacy #1: Affirming the consequent
These types of truth claims are consistent in the evolution genre. The first, and most important fallacy is that these arguments affirm the consequent. This fallacy states that if P implies Q, then Q implies P. For instance, if a theory predicts that it will rain next Tuesday, that does not mean that if it rains on Tuesday the theory is true. But this is precisely the logic of evolution. If evolution is true then we expect fossil sequences and genetic similarities to fall into the expected evolutionary patterns. Evolutionists such as Carroll and Myers have found such patterns in the fossil and molecular data and claim, as above, that they prove evolution to be true.
Fallacy #2: Confirmation bias
A common motif in the evolution genre is the elevation of confirming evidence. As in the examples above, the patterns that fit the evolutionary expectations are touted as proof texts. But there are plenty of evidential problems as well. Often these problems are in the same data in which the evolutionists find their persuasive patterns. Yes, many fossils fall into the expected pattern, but many do not. Likewise for the molecular data. These uncooperative data are often not considered when evolutionists formulate their proofs of why evolution is a fact. This fallacy is known as confirmation bias.
Fallacy #3: Evidence denial
Because there is so much uncooperative data, evolutionary expectations have become quite flexible. In fact, sometimes it is difficult to identify just what constitutes the expected evolutionary pattern. In the fossil record, for instance, increasing complexity, decreasing complexity, rapid appearance, trees, bushes, diversity explosions, stasis for eons can all fit within evolution's broad and flexible imagination of what natural forces can do. Therefore, when evolutionists find great significant in evidences that fulfill some particular evolutionary pattern, they are ignoring the many other patterns that evolution also expects.
Evolutionists consistently make eye-brow raising claims. Evolution, they say, is a fact beyond any shadow of a doubt, as obvious as gravity, and so forth. These claims are perceived to have the full faith and backing of modern science. But they do not. Behind such unbelievable claims is, not surprisingly, any number of logical fallacies that cannot stand up to even modest scrutiny.