What difficulty are you playing?
On Tactician there are plenty of opponents with evasive aura (which they don't have on Classic). This makes a pure physical more problematic.
You also have the demons in hall of Echos - one 100% immune to all magic and one 99% immune to physical.
There are also the
Horrorsleep mirrors with 100% Resistance to everything but Earth and Physical, which they only have 98-99% Resist to
.
I would actually call those demons a case of Bad Design because it forces you to have both sources of damage on your main character without any warning that would be necessary.
Luckily for me (solo scoundrel) the skill Sawtooth Knife (unlike all the others) doesn't count as physical when it comes to resistances - it directly hits vitality even though the tooltip says piercing. That surely must be a bug assuming piercing damage is physical.
I don't think it's a bug. I think it's perfectly intentional. Piercing Damage ignores all armor and resistances, that's it's whole thing. And it only matters for that one enemy in the entire game (can't target the M-you-know-whats with skills).