We already had a discussion about physical damage and armor ignore mechanics back in Mogu'shan Vaults at Spirit Kings.
Will repeat myself again, there are mechanics in Mists of Pandaria which ignore armor. This requires a more detailed investigation than "logic" or "it's physical damage" for each spell individually.
For example https://www.db.pandawow.me?spell=122409/korthik-strike deals 150'000 damage on normal mode. On this timestamp
we can see that player got hit for 135'000 damage. Might not be the best example, but there is a chance these trash mobs are affected by https://wowpedia.fandom.com/wiki/Weakened_Blows (since they have a warrior in raid), which explains why player took 10% less damage than base amount.
So please, review each spell individually and update your report. Like I said, just because it's physical damage doesn't mean it will always take into account your armour.