Because they're scientists with more knowledge of physics than you or me?
I don't understand why you'd automatically assume they haven't measured the same neutron.
Because, quoting the article:
In this experiment, the neutrons pass through a magnetic field to ensure that the spins are aligned in the same direction.
Nice, get a couple of them, guaranteed to have the same magnetic properties. Sounds fine. Lets go on.
They then enter the interferometer where the beam is split so that the neutrons pass down both arms of the device before recombining to produce an interference pattern picked up by a pair of detectors.
Fine. Split them up like a normal double slit experiment. As stated, neutrons in both arms.
But now we have a paradox?
The paradox arises when the team carried out two weak measurements. The first found the presence of neutrons in one arm while the second noted their magnetic properties in the other arm.
As stated above, there are neutrons in both arms. They find evidence of presence of neutrons in one arm (obviously, since they are in both arms) and measure magnetic properties in the other arm (obviously, since there neutrons there as well).
The result is so blatantly obvious. And there is no reason given in the article to assume both measurements apply to the same neutron. Its not like there is an explanation i dont understand, i could live with that, there is no explanation given at all.
Perhaps they have got it wrong; time will tell. I think it's safe to assume that at the very least they remembered to rule out the obvious alternative explanations before publishing.
Perhaps they have ruled out the obvious explanation. In that case the article is utter crap for not mentioning it.