Why did Nehemiah pluck out the hair of Israelite men?

Because they married non-Israelite women

(Or allowed their sons or daughters to intermarry)
I contended with them, and cursed them, and smote certain of them, and plucked off their hair, and made them swear by God, saying, Ye shall not give your daughters unto their sons, nor take their daughters unto your sons, or for yourselves. Nehemiah 13:25