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We know Yamato and Ace must’ve fought, as Luffy’s combat style and spirit reminds Yamato of Ace.

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That being said, I have a theory as to why they clashed.

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At this time Ace was not part of Whitebeard’s crew, which means he was probably still hunting Whitebeard to kill him and make a name for himself as an up and comer.

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Maybe Ace expressed this desire to Yamato, that he was in the New World to go after Whitebeard. Yamato, recognized the name Whitebeard from Oden’s journal as a captain and comrade, so in the Oden disguise she perceived Ace as an enemy and they clashed.

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To Yamato, she was defending Oden’s former captain Newgate. It is what Oden would have done.
*Theory by ahood34