Well... it's a tough answer...
Honestly there probably isn't any science behind it. If I had to guess though, it's because it's a very specific magnetic field that needs sufficient strength to cause evolution. It might be the interaction of several dozen magnetic fields to create the magnetic field needed for Magnezone to evolve, and it's condition's may be nigh impossible to create in a laboratory setting.
I have a few more ideas. Since I dunno the conditions of what created ZEL -- I stopped playing after episode 11 or so, and even then I don't really remember much -- I'm going to assume that the magnetic fields created... it... in some way, and not some freak explosion or something to do with a reactor or somethin'.
In the real world, black holes can have a charge and a magnetic field. However, uncharged black holes cannot. If there was a flurry of charged, microscopic, black holes, it could cause some utterly strange things to happen. Of course, the hawking radiation would be immense, and it would be like a nuke going off.
Something like a naked singularity would certainly be incredibly strange, since it's a point of infinite density, and yet it's not hidden behind an even horizon. This has to assume that loop quantum gravity is correct. Since theories predict a naked singularity could produce light, it's reasonable to extend it to producing magnetism, since according to quantum electrodynamics, magnetism is the propagation of virtual photons. Certainly, a naked singularity would be utterly insane, and I cannot even began to predict the effects, but perhaps it persists in the Pokemon world somewhere... of course, this assumes loop quantum gravity is correct, and the cosmic censorship hypothesis is incorrect... which is a pretty strong conjecture as it stands right now, and it's unlikely to be wrong.
There's also magnetospheric eternally collapsing objects (MECOs), which are essentially black holes that never fully collapse. These could produce some wicked magnetic fields, and we aren't actually sure of the effects of them, and they aren't proven yet. However, they are strongly plausible, since normal black hole formation requires that matter move faster than the speed of light, violating one of the most successful scientific theories ever. These may so-called quark stars as well.
It may a naked quark or even, if they exist, naked preons. These shouldn't exist, but the standard model is just a theory, and there are problems with it. It could be some new exotic particle that causes it, something like a glue ball perhaps.
Potentially a magnetar/neutron "star", if it was tiny, could cause something of this effect. Extreme gravity combined with magnetic fields that could rip iron from your body from 100,000km away would produce some... ahem... stellar affects.
There's the possibility of a wormhole or a tear in spacetime. In the real world, white holes are considered a possibility, and they're the opposite of a black hole, nothing can go in them, and they may be the "other side" of a wormhole. In Pokemon, a strange phenomena caused by one of the creation trio could be cause for this.
Finally, and really the explanation I'd go with, something like a closed-time-like loop could be cause, and in theory, be created by Dialga. CTCs allow for events to occure without a cause, and break causality, so some event could have preceding cause. If these places with strange magnetic fields were actually a CTC, it could cause spontaneous fusion, without an actual cause in normal reality.
Or in all of this, I'm just over analyzing and being strange. It is Pokemon after all; there's no real way to explain it, so I was just spitballin' here and throwing out everything I could think of. There is one more particle I wanted to talk about, but I can't remember it. It's a gravitational wave that loops in such a way as to be a particle.
So in essence, there is no answer. Becuase its Pokemon.