As much as i love the Lunar Rebellion one thing always got my head scratching. And that is Valiant Doo.

Both Pegaspolis and Unicornia fought over jurisdiction on the trial and mine thinking is. Woukdn't that be already settled in the Accords? I can't see the founders of Equestria not seeing this issue come up.

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There were no doubt rules written up, but when there’s rapidly escalating tensions on the way to civil war not everyone cares about the letter of the law.

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but you think somepony would mention it.

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Laws, treaties, and agreements only work as long as everyone agrees to follow them. Issues started to come up with many pegasi felt that Valiant was justified in killing that unicorn due to besmirching pegasi honor, and thus didn't feel they needed to have him face any kind of justice. Naturally, the unicorns disagreed.

And in the end, everyone agreed that a duel (a socially acceptable way to deal with disagreements like this) would settle the matter.

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Yet Rightly was willing to do a trial. Granted again Celestia had a chance to end this by INVOKING the law but didn't. thus why I put this version of elestia's in the worst list that isn't evil.

Celestia's largest flaw in the Lunar Rebellion was a complete disconnected with 2/3rds of her people. She is clearly the main architect of the civil war, through her incompetence of nothing else. I'm not going to argue otherwise.
However, her second flaw that is almost, if not as bad, is her unwillingness to use her power / authority, for fear of abusing it. These two flaws combined I think is a large part of why the law didn't come up.
I suspect that the law would defer to Pegaspolis on the matter for Valiant to stand trial under their traditions as one of their citizens. However, this would not have satisfied the unicorns who wanted their own justice. This is where the weak rulership and incompetence come in: Celestia would almost certainly not be willing to directly, and publicly, countermand her subjects without an overriding moral imperative. Especially with her (implicit) favorites, the unicorns.
That is I think the most likely explanation, and not one we would ever get from the biased author, since it paints in no uncertain terms Celesta's massive flaws.