As suspected, the damage is from the class bonus. Note the +1 that's across all melee weapon types. Compare what the details show you with what your traits would otherwise give.
STR 0 with AGL 3 would give only +1 with 1-H weapons, not the +2 that is shown. That extra point is from the class bonus. Agility gives an increase to 1-H for every 2 points, rounding down ( at AGL 2, 4, 6, etc, with no increase for 3,5,7 etc).
STR 0 with AGL 3 would give +3, not the shown +4 to damage. Agility has an one-to-one ratio for extra damage with Light Weapons. Zero STR so nothing there.
Ranged weapons DON'T get the class bonus so the damage from AGL is as expected. Note that Rogues have skills that increase bow damage.
So everything is as expected. You'll see another few class bonus as stated above.