The science i've seen done in university labs does not follow the kind of rigor you're talking about. Much of the time, you simply need to get "pretty close" to best practices.
The biggest indicator that the machine was the likely culprit (without considering any of the factors you mention) was that the experiment had been proven in the past to work, with a control group for comparison. Add to that the other mice that were doing fine that were away from the machine, and that the mice close to the machine got better when it was turned off. It's not "scientific" per se, but it makes more sense than any other reason that anyone could come up with for this scenario.
To deal with this in future projects, a researcher could take an approach that treats everything as a set of systems, and examining every part of each system for potential problems. But I doubt anyone's getting paid well enough to do all that for every experiment. But it is reasonable that if you're doing an experiment that depends on a bunch of other experimental results, you do your due diligence and vet all the information and results.
The biggest indicator that the machine was the likely culprit (without considering any of the factors you mention) was that the experiment had been proven in the past to work, with a control group for comparison. Add to that the other mice that were doing fine that were away from the machine, and that the mice close to the machine got better when it was turned off. It's not "scientific" per se, but it makes more sense than any other reason that anyone could come up with for this scenario.
To deal with this in future projects, a researcher could take an approach that treats everything as a set of systems, and examining every part of each system for potential problems. But I doubt anyone's getting paid well enough to do all that for every experiment. But it is reasonable that if you're doing an experiment that depends on a bunch of other experimental results, you do your due diligence and vet all the information and results.