As other comments observe, the replication crisis predates the use of ML, so the causes are clearly deeper.

I think there's actually a very simple explanation for this which lots and lots of people hate, so they're sort of in denial about it. Academia is entirely government funded and has little or no accountability to the outside world. Academic incentives are a closed loop in which the same sorts of people who are producing papers are also reviewing them, publishing them, allocating funding, assessing each other's merits etc. It's a giant exercise in marking your own homework.

Just looked at in purely economic terms, academia is a massive planned economy. The central planners (grant bodies) decide that what matters is volume and novelty of results, so that's what they get, even though the resulting stream of papers is useless to the people actually trying to apply science in the real world ... biotech firms here but the same problem crops up in many fields. It's exactly what we'd expect to see given historical precedent and the way the system works.

There's another huge elephant in the room here beyond the replication crisis ("to what extent are the outputs wrong") which is the question of to what extent are the outputs even relevant to begin with? Whenever I sift through academic output I'm constantly amazed at the vast quantity of obviously useless research directions and papers that appear to be written for their cleverness rather than utility. The papers don't have to be wrong to be useless, they can just solve non-problems or make absurd tradeoffs that would never fly in any kind of applied science.

I read a lot of CS papers and I've noticed over time that the best and most impactful papers are almost always the ones coming out of corporate research teams. I think this is because corporate funded research has some kind of ultimate accountability and connection to reality that comes from senior executives asking hard questions about applicability. For instance in the realm of PL research academia pumps out new programming languages all the time, but they rarely get any traction and the ideas they explore are frequently ignored by the industrial developers of mainstream languages because they're completely impractical. This problem is usually handwaved away by asserting that the ideas aren't bad ideas, they're just incredibly futuristic and 30 years from now we'll definitely be using them - but this kind of reasoning is unfalsifiable on any kind of sensible timescale so it's the same as saying, "I shouldn't be held accountable within the span of my own career for how I spend tax and student money".

As time goes by I am getting more and more sympathetic to the idea of just drastically cutting academic funding and balancing the books by drastically reducing corporation tax. The amount of total research would fall significantly because corporations wouldn't invest all the newly available money in research, or even most of it, but it's unclear to me that this would be a bad thing - if 75% of research studies coming out of academic biotech are wrong then it stands to reason that if standards were improved significantly, funding could be reduced by (say) 50% and still get a similar quantity of accurate papers out the other end. It's possible the science crisis is really just reflecting massive oversupply of scientists, massive undersupply of accountability and in general research should be a much smaller social effort than it presently is.