Yah augmentin does that...my girl was given that for tonsilitis and she had diarrhea as well. Augmentin causes diarrhea in adults (me!) as well >.< but once stopped the course, ok already.
it's more important to complete the antibiotics
just make sure your child stays hydrated, and after completing the antibiotics, you can feed him some yogurt to help replenish the good bacteria in his body