Shaymin vs EX Pokemon

Hey guys, I came across an issue the other day that I thought was weird, I had a Shaymin on my bench, this is to prevent bench pokemon from being damaged by an EX pokemon, my opponent using a Dragapult EX managed to use phantom dive and took out a Psyduck on my bench. Now I thought that the ability of Shaymin was meant to stop that from happening, so now I'm wondering if there is any point in having this pokemon in my deck. To me it reads that any pokemon without an rule box cant be hurt whilst on the bench, but this attack still managed to take out a benched pokemon, that doesnt have an rule box such as the psyduck with the ability damp.