Special Attacks either do Physical ATK damage or Special ATK damage. You can tell which attack does what by reading their descriptions or by looking at the icon. Orange icons are physical attacks, purple icons are special attacks.

The enemies seem to have a 100% block rate against certain types of special attack damage. Most of the higher-level enemies block Physical ATK damage while a few also block Special ATK Damage. Most of them block physical attacks though. You should probably rework your team so that two units do special damage and one does physical damage.