Whilst Rufus may have thought he had things 'sorted' to enable him to lie low at Marcus's house, Mac2 had deduced that it needed to sort out Rufus. It was concerned about recent inconsistencies in the boy's behaviour. From an objective Mac2 perspective, Rufus had made mistakes, putting the machine's existence somewhat in jeopardy.
For instance, Rufus had verged on kindness with Beth in letting her live and now he had lost touch... and there would be a baby shortly too. Also, Rufus had been sloppy with the newspaper reporter and now she had really stirred things up.