Bones was saying that it was up to her to decide if the procedure was being abused, not up to the aurors whose job it was to implement it

The specific error the Auror was making (if we are to take a consequentialist look and ignore the settled rules) was to act on a hypothetical problem that turns out not to be real, so Bones's superior expertise would be used, in particular, to determine whether the hypothetical problem is real.