It has long been a joke that every bug in Microsoft products was defended by the PR in Microsoft as "it's not a bug, it's a feature" no matter how annoying/dangerous the bug was ("my files disappeared" "It's not a bug, it's a feature: self-cleaning OS!").
Here, Roy is using the same words to explain that Belkar, one of his own teammates, having been affected by a "friendly fire" (i.e. a spell cast by his own team) is not, in fact, a problem, but an advantage for Roy's plans.
Grey Wolf