Agamaggan Counterspell double value

I just had an incident where I casted a spell using Agamaggan’s ability and had what I believe to be an unintended effect. Despite being countered, the spell (Shaldrassil) still dealt 7 damage to my opponent. This isn’t the issue since counterspell still takes mana in other scenarios, but what I think IS an issue is that Agamaggan’s effect was still present. Despite 7 damage already being dealt, I could then play a 2nd card also using my opponents health.