I'm fighting some a rank 124 ( i'm rank 156)

I use spy probes and the probes tell me he has 1900 attack and 2000 defence

My ship has 3300 attack and 1500 defence.
His a Aerlen Fixer , I'm a Vygoid Excavator, neither of us have artifact buffs ( he has trinity drives though ).
His a Tita, I'm a Goliath

Even though my ship is more powerful, his doing double damage to me.
Any ideas why this might be happening? :S

Damage Cap. You have more decks (Goliath > Titan) so you have a higher damage cap (Decks/2). Damage cap is a factor in the calculation.

Could there be other reason Darth Flagitious?

His a Titan so he has > 700 decks, so his damage cap is 350, so maybe damage cap is not the reason. I still only do 80 damage, he inflicts about 160 back, his attack is 400 higher than my defence. my attack is about 1000 higher his defence.
Do these spy probes provide me his defence including his Race and module bonus's?

The probe does not take into effect the Trinity Core Drive's effect.

Higher dam cap means person will do more damage with the same attack, not just the limit they can damage you.

Could also be the difference in scan / cloak. If his scan is higher than your cloak he crits you. The greater the deprevity between scan / cloak the more often a crit occurs.