Are they malicious or incompetent? Yes, maybe, no, none of the above, both, and “it depends.”
In the initial case - first time the doctor writes the script without allowing for nurse input, or first time the CEO adds friction, perhaps unknowingly, to the operations of the company - it would most often be simple ignorance, not even incompetence.
After a few times of being told there is a better way - doctors could ask the nurses which method the patient responds to, or the CEO could ask their subordinates what problems could be caused by intended choice - and they fail to modify their behavior, it progresses into probable incompetence. If, after reaching that stage, when confronted by the reality of the choices they take corrective action, it remains mostly incompetence as they continue to repeat the same mistakes. They’re willing to correct the problem when it happens while seemingly being unable to predict that it will happen, again, for the same reasons as the last time, or the last dozen times.
On the other hand, after learning of the consequences, refusing to change behavior, and refusing to correct the current situation - the doctor indicates that it will be pills as written, regardless of the patient’s adaptability, or the CEO indicates that if the friction is too much the staff can just leave - it’s not mere incompetence. It might not be actual malice, which would require knowing more than general information. It could, rather, be an egotist’s drive, or a sociopathic disregard for others, or any of several other possibilities. It could, of course, be simple malice. Of course, even at the first point it could be malice, or any of the other possibilities.
The likelihood that it is malice is low in the beginning, as there are other options. As the other options fall one-by-one, like tin soldiers in a storm, the probability of malice increases. As advised by Sherlock Holmes, “Eliminate all other factors, and the one which remains must be the truth.”