The linked paper is a very nice overview. Of course there problems are known and there are people trying to fix all of the issues (mostly in the relative obscurity of non-overhyped corners of academia), but the concise example-guided description of these problems is great.
Somehow I think the most fundamentally damning critique, and causality shares this problem, is also the most vague. That applied scientists/experimentalists look at the "automation" that these approaches are supposed to enable and say "that's either doing the trivial part of the job or giving you BS answers".