There are many, but macro evolution (the fundamental change in DNA from one species to another reproductively) as a whole is speculated and not shown to be reproducible.
There are also fundamental challenges involved with the initial spark of life, even the simplest organisms take a lot of predefined processes within the cell structure, involving 30+ mechanisms to feed the cell, divide etc, so how this first set of organisms initially were able to even survive, let alone evolve such processes, is a key issue with the 'true' evolution theory (that the primordial pool evolved life).
Ontop of that, there is a bunch of subset issues around the genome project failures to prove links between species in terms of DNA, the underlying lack of proof (fossils) of animals that would of evolved between species (i.e. the theory is that horse like creatures evolved slightly longer necks to get more food, and over time (a long time) this advantageous evolution produced giraffes, but we have never found a skeleton of a slightly long necked giraffe or intermediary)
There is also no proof currently, that as evolution stated, mutations are random. The mutations we have been able to observe first hand (such as E.coli evolving to be able to live in acidic environments for instance) have been very reproducible, and in fact, have actually been tracked back to dormant DNA, thus in at least some sense, non-random, as genetically the species is already capable of it. Other evolutions we can observe show the processes of evolution, but we haven't witnessed them first hand, or been able to reproduce them (a key element of the scientific process)
I'm not saying I don't believe in evolution, in fact the opposite, I definitely believe in evolution, but if you choose to ignore the scientific process and look for the evidence/observations which can help improve, or even disprove, the thoery in order to make our understanding more comprehensive, then you are anti-scientific like the article states.
