In lieu of actual fraud or a methodological mistake that wasn't represented/caught in peer review, it's still extremely difficult to control for all possible sources of variation. That's especially true as you go further "up the stack" from math -> physics -> chem -> bio -> psych -> social. It is absolutely possible to honestly conduct a very high quality experiment with a real finding, but fail to account for something like "on the way here, 80% of participants encountered a frustrating traffic jam."
Their finding could be true for people who just encountered a traffic jam, and lack of replication would be due to an unsuccessful generalization from what they found.
In what sense do they not? On the assumption that there can be other "worlds" for which math, but not physics, holds?
A geology that isn't anchored to our physical reality seems intrinsically invalid.
But it also doesn’t make it not false. It makes the null hypothesis more likely to be true.
The other is the introduction or loss of critical cofactors or confounders that radically change environment and context.
Think of experiments of certain types before and after COVID-19.
This is a subtle point, but truth or falsity isn't really the issue. The problem with a non-replicable study is that the rest of science can't build on it. You can't build your PhD on top of a handful of studies that turn out to be non-replicable, and so on. It is true you can't build science on outright false statements, either, but true statements that aren't adequately reproducible are also not a solid enough foundation. That may seem counterintuitive, but it comes down to this truth not being binary; even if a study comes to a nominally true conclusion it still matters if it didn't do it via the correct method, or is somehow otherwise deficient in the path it took to get there. Studies are more than just the headline result in the abstract.
But the whole process of science right now is based on building up over time. How could it not be? It has to be, of course. But non-replicable studies mean that the things you're trying to build on them are non-replicable too. It doesn't take all that much before you're just operating in a realm of flights of fancy where you may "feel" like you're on solid ground because of all the Science you're sitting on top of, but it's all just so much air.
However, it is also true that non-replicability is a signal of falsity, and that is simply due to the fact that the vast, vast, vast, exponential majority of all possible hypotheses are false. As is another subtle point, a scientist engaging in science properly should probably not come to that conclusion and may not want to change their priors about something because of a non-reproducible study very much, but externally, from the generalized perspective of "what is true and is not true" where science is merely one particularly useful tool and not the final arbiter, I may be justified in taking non-replicable studies and updating my priors to increase the odds of the hypothesis being false. After all, at the very least, a non-replicable study tends to put an upper bound on the ability of the hypothesis to be true (e.g., if someone studies whether or not substance X kills bacteria Y, and it turns out not to reproduce very well, the lack of reproducibility does fairly strongly establish it can't be that lethal).
This isn't true at all. You could have future experiments set out to prove the opposite, or to dig into what novel and confounding variables are at play causing conflicting results. The fact that you have studies that inconsistently replicate is actually a sign of possible new knowledge if you can find out which undiscovered variable is causing the conflicts. Especially in medicine, you can have a case study that leads to future studies even though that specific case may not be able to be consistently replicated in other n=1 populations.
"e.g., if someone studies whether or not substance X kills bacteria Y, and it turns out not to reproduce very well, the lack of reproducibility does fairly strongly establish it can't be that lethal"
Or there's another factor that hasn't been discovered, such as back in the day before understanding gram positive and negative bacteria was even a thing. If you don't know the subtypes exist, you would see inconsistent results as that is an undiscovered variable that you can't possible account for until it's discovered. Once discovered and controlled for, the substance could be very lethal.
Just because a study doesn't replicate, doesn't make it false. This is especially true in medicine where the potential global subjects/population are very diverse. You can do a small study that suggests further research based on a small sample size, or even a case study. The next study might have a conflicting finding, but that doesn't make the first one false - rather a step in the overall process of gaining new information.