They can out speed with slower move 1 in some modes were initiative is split like Surviva and Matsuri, they have their normal initiative but you have your total divided by 4 and given to each ninjas, which in 99% cases makes your move 1 slower. Few other game modes also do this.

But if it's happening in duels/gnw then it could be lag, try auto like someone above said and see if it still happens in a duel.