Judging from the replication crisis in many fields, maybe getting a PhD doesn't teach the scientific mindset as much as we'd hoped.
If you don't reward (By issuing grants for) negative results, or null results, or replicating prior studies, why do you expect that scientists will aim for any of those outcomes?
You have to eliminate a lot of possibilities in a universe with this much detail
The real issue, again IMO, is more of an “expectation crisis”. We expected to repeat this and failed to. Because we’re still a ridiculously ignorant species lacking conscious awareness of many aspects of reality