Minor Plot hole: Tamina is the leader of the city-state of Alamut but she is still considered a princess rather than a queen even if she has no husband and no remaining living family members.
Minor Plot hole: In Prince of Persia, robes can be poisoned. Poison can cause combustion of human flesh but NOT the robe itself. Poison does not burn upon contact but after several minutes (ancestor of timed-bomb). And robes have the magic ability to seal the wearer in like a Venus flytrap.
Minor Plot hole: Dastan army's help him climb a fortified-wall by creating a ladder made-out of crossbows bolts and instead of firing the bolts in advance; they shot the walls WHILE Dastan is climbing the unfinished ladder. Furthermore, how can crossbow bolts pierce through brick walls?
Minor Plot hole: When Nizam finally got possession of the dagger of time; he decided to guard it by one deadly assassin instead of a dozen average soldiers or instead of keeping it with him. Since he knew that roughly 4 people were potentially going to try to steal it; he could have made it impossible for one knife-thrower to do it from his highest tower.
Super Plot hole: Nizam, the antagonist, wants to go back in time in order to let his brother die so that he can become king instead. The only thing he needed to accomplish his goal was to take the dagger of time from Dastan. Since Dastan had always trusted his uncle Nizam, he could simply have asked to study the dagger instead of elaborating a complex regicide to frame his nephew in order to obtain it.