To detect design, or determine whether it is good or bad design, we need to know what the goals of the design are. For that matter, determining whether mutations are detrimental or not often depends on the situation. If God’s goal is to create a dynamic, adapting, diverse suite of organisms, using some basic physical patterns and mechanisms, then evolution does that rather well.
Obviously, not everyone is predestined to be Reformed; there exists a range of views on the degree of prior specifying and determination that God uses. But both our science and theology need to be driven by the data rather than by what we might want to be true. God is the way He is; ultimately our ideas about Him are either right or wrong in any particular detail, just as natural laws are not subject to our preferences. In many cases, the data are relatively sparse, and we’re left with question marks.
In John 9:3, Jesus declares that the man born blind was blind not because of some sin but in order to to display the works of God. Similarly, Joseph perceived God working for good through the evil actions of his brothers. Habakkuk, Ecclesiastes, and Job struggle with these questions. Paul sought freedom from whatever his “thorn in the flesh” was. Yet we are not given a detailed account of how this works out in systematic theology. We are assured that God is in control, that He is working a plan for good, and that He knows our sorrows and sufferings. But we are not told why not have things turn out some other way.
Human sin does contribute to problems, even prenatally - substance abuse, stress, and pollutants can negatively impact development. But must humans be so wicked and stupid? Especially, couldn’t I be less wicked and stupid? Being less stupid tends to go with being more aware of the problems in the world, though.
Both the biblical accounts and other historical data, including personal experience, indicate that physical miracles are rather rare events. Even in the process of salvation, God works primarily through the process of having people telling other people or reading rather than miraculous communication. Similarly, we are tasked with working to try to help to address problems, whether medical, social, etc. Why couldn’t there be fewer of them? Why can’t the problems be less exhausting? Why can’t we have consistently good supervisors rather than self-centered rulers? We aren’t told.
Although Jesus did plenty of healing, He also had points of trying to avoid the crowds to focus on more important issues. God’s priorities are evidently often different from ours. If we accept that His grasp of the situation is better than ours, we can trust that things are working for good even though we don’t see it. In C. S. Lewis’s The Pilgrim’s Regress, the main character is told that he had in fact come by the shortest route, but it would look odd on a map.