He leads his army to their death beds, which not only greatly decreases their chance at winning the war but also just results in so many deaths. He knows that the mongols are not fighting with honor, yet he still feels the need to fight them with honor knowing full well he is endangaring his own people. This obviously backfires and leads to a lot of his people's deaths.
He always looks down on Yuna even after everything she has done for him. Yuna literally helps rescue Shimura and even after getting rescued, Shimura treats Yuna horribly and refuses to let her leave, forcing her to risk her life in servitude of him
Now an argument can be made his previous actions aren't necessarily villainous but rather within his own beliefs and morality, but the follow reasons really push him into villain territory imo.
He imprisons his own nephew, Jin and this results in his horse's death later in the story when Shimura's men shoots his horse down.
He tries to literally frame Yuna for the ghost in order to preserve his own self-image and keep himself out of trouble. If he went ahead with framing her, Yuna would literally be executed. So Shimura is willing to execute an innocent woman just for his own self-interests. Also worth mentioning that Yuna literally helped him break out of prison, and he is willing to frame her despite everything she has done in servitude of him.
Nail in the coffin is when Shimura is willing to murder his own nephew once he gets orders from higher ups, knowing full well his nephew is the reason they won the war.