Here is what i'm thinking.
Yamato is close to Ace.
And then when she know if Ace gonna be executed, she want Kaido to came to marineford to save Ace.
And then, Shanks stops him for coming to Marineford.
After that incident, Yamato became rebellious.
Thats why she had a handcuffs in her wrist.
Shanks is a villan confirmed.