For one, the narration alludes to the fact that she pitted her minions against the duo so that she could study how they fought: their aggression, pace, style, etc.
[sarcasm]Wow! Holy crap, there was no way she could lose with that kind of invaluable knowledge.[/sarcasm] Please...
While this doesn't automatically grant her the win - which she earned through superiority as a fighter - it is something to account for in the battle.
As a factor, it is tiny when you consider the other variables; fatigue, injury, how powerful the actually are.
Secondly, where the hell was Kit shown to be either wounded... Unless you count singing the heel of his boot
Refer to the [bold]. In fact, here's the exact quote.
The underground lake's surface reflected flashes of red and yellow lightning as the energy field confining Obi-Wan and Kit Fisto lessened for an instant. He felt pain and fire as he lunged through, his lightsaber absorbing enough of the energy to keep the shield from frying him. It snapped back on swiftly enough to singe Kit's left heel as the Nautolan jumped free.
This would affect his footing and movement, which would be a huge deal in a saber duel.
or considerably fatigued... and beating down goons as causes for said hinderances.
Refer to the [bold].
But seriously, it was more than just 'beating down goons', judging by the descriptions, Fisto was putting in a hell of an effort in defeating them, that king of sh1t would tire him.