I had one day of this problem....it was a windy/chilly day, and there was a trailer where it wasn't supposed to be. Well, Ice just about had a cow in the round pen, charging through the whip, kicking out at it, turning his butt to me.....I pushed him through it and 45 minutes later he finally found his brain and gave me a nice turn in and stopped acting like an idiot. Did I mention he's 11?
Sounds to me like your three year old is just being a three year old. Push him through it and keep working with him on the lunge line and eventually he'll get it.