It could be that the boys somehow provoked the butcher or got in his way. Or perhaps there's a deeper, darker backstory to the butcher's actions that hasn't been fully revealed yet.
Butcher manages to kill Homelander through a carefully planned and executed strategy involving a combination of surprise attacks and exploiting Homelander's weaknesses.
The butcher in the comics kills the boys in a brutal manner. He takes advantage of their vulnerabilities and employs various weapons and strategies to ensure their demise.