Magneto goes to the plant to kill those guys, and Apocalypse just randomly shows up and kills them first. This big emotional moment that the movie had been building up to just becomes a "Look how dastardly this bad guy is!" moment.

And that was the last time in the entire movie that Magneto was a real character and not just Apocalypse's boring lackey. The perfect example of how Sony consistently squanders perfectly awesome characters for boring, two-dimensional plot devices.