See, I'm fine with warning them they're getting close to jumping offsides and whatever. But when a ref sees a violation committed, it's too late IMO. If they saw the guy about to run on the field and stopped him- I don't even think I'd be okay with that, but I sure don't think that should just be a warning when they have that kind of penalty with it.
If it's not a big deal, don't attach that kind of penalty with it. The ref's actions and the rulebook seemed to contradict each other.