[Emperor's Child]

Maybe he is just plain out-shooting you. Find out if you have equal or better combat sensors / ECM compared to the enemy, and what his racial offensive and defensive modifiers are.

I'd hazard a guess that he has advantages on you in both areas. You can also look to see if he has any armor that gives him defensive benefits, with both at level 3 his ships will have an additional 30% defensive modifier.

If you were playing against a human opponent I'd also suggest looking at his fleet and crew training levels, but you could not do that unless you captured his ship (for ship training).