I've noticed the same thing when doing tests... with both missile units and melee. Whichever I control performs marginally better, even when the task is as simple as advance to range and begin firing or advance slowly and charge.

The AI often advances closer than maximum range before firing, also it often reforms it's men while taking fire... this means the human player gets crucial initial kills, and more volleys off in the same amount of time. With melee troops the AI seems to sometimes approach at funny angles and/or wait too long before charging... the end result being that whichever unit the human player controls performs better.

This isn't really that important of an issue when you're considering campaign play, it would only matter if you're doing research for multiplayer battles. If the longbows win as long as you're controlling them... well, that's all that matters.