First things first: what are mutations? They are accidental changes to an organism’s DNA; they typically happen when the cellular machinery makes a mistake as it copies DNA from one cell to the next. Once a mutation happens, it may or may not be preserved down the generations — whether it is depends on a variety of factors, not least natural selection.
Some proponents of intelligent design claim there is no evidence for continuing evolution in modern times. This article seems to be making a good case that there is. I have no doubt that evolution has happened and is continuing to happen (even if at a slow pace). The real question that I think needs answering is if the mechanisms that are in place to drive evolution are by design or by random accident.