Adam Clarke on Exodus 32:28

There fell about three thousand men - These were no doubt the chief transgressors; having broken the covenant by having other gods besides Jehovah, they lost the Divine protection, and then the justice of God laid hold on and slew them. Moses doubtless had positive orders from God for this act of justice, (see Exo 32:27); for though, through his intercession, the people were spared so as not to be exterminated as a nation, yet the principal transgressors, those who were set on mischief, Exo 32:22, were to be put to death.