The reason this is different to the Dark Dragonite is because the Team Rocket set did contain a non-holo Dark Dragonite.
Since the design process of the cards would include what the cards look like, rather than including details such as are the cards holo, this error almost certainly occured by someone copy and pasting the design from the holo sheet template to the non holo sheet template and forgetting to change the number. The Dragonite was always intended for it to be on the sheet, just a small detail was unchanged.
The Magneton did not have a non-holo version, so in order for this error to be real, someone would have had to create an entirely new sheet template for non-holo cards, or replace one of the existing non-holos with Magneton.
Dark Dragonite could have got through quality checks, because the number is something that is hard to notice unless you are actually looking closely, so if someone was comparing what the cards should be to what they look like, it's easy enough to slip through. If a sheet suddenly had Magnetons instead of Beedrills, people would notice.
The only other option would be if a full sheet that was supposed to be holo, was printed non-holo instead. If this was the case, there would be 110 of these errors, and some would almost certainly have popped up by now.
So, you can understand our skepticism.
Not saying impossible, not without seeing the card.
Just incredibly unlikely.