I believe you're referring to shield mods that bosses can have. They can have Material Shields, Elemental Shields, Occult Shields (you'll see these named in their list of mods). They can have more than one of these shields and so if you do mostly or all material damage you won't necessarily break through the elemental or occult shields in the time that it takes to kill the boss.

Trulain

Many thanks. Someone over at reddit also explained it and this is indeed right. I should start to pay more attention to those elite mods that strong enemies have, i always just whale on them without realising what those mods were.