John Gill Commentary Psalms 99:8

"Thou answeredst them, O Jehovah our God: Thou wast a God that forgavest them, Though thou tookest vengeance of their doings." — Psalms 99:8 (ASV)

You answered them, O Lord our God
This is repeated to show the certainty of it, and to encourage the people of God, in all ages, to pray unto him:

you were a God that forgave them ;
even Moses, Aaron, and Samuel; for, though they were great and good men, they did not live without sin, and stood in need of pardoning grace and mercy, which they had; or rather the people for whom they prayed: so the Targum, ``O God, you were forgiving your people for them;'' that is, through their prayers; see (Numbers 14:19Numbers 14:20) (Psalms 78:38) ,

though you took vengeance of their inventions ;
their sins, which are the inventions of men, (Ecclesiastes 7:29) . Kimchi and others interpret this of the inventions, designs, and practices of Korah, Dathan, and Abiram, against Moses and Aaron, (Numbers 16:32Numbers 16:35) but though God took vengeance on them, it does not appear that he forgave their iniquities; therefore it is best to understand this either of the sins of Moses and Aaron themselves, which, though pardoned, God took vengeance of, and showed his displeasure at, by not suffering them to go into the land of Canaan, (Numbers 20:10–12) (Numbers 27:12Numbers 27:13) ,

or else of the sins of the Israelites, who murmured upon the report of the spies; and though they were pardoned at the intercession of Moses, yet so far vengeance was taken upon them, that none of them were suffered to enter the land of Canaan; but their carcasses fell in the wilderness, (Numbers 14:19–23) ,

and thus, though God forgives the iniquities of his people, for the sake of his Son, yet he takes vengeance of them on him, their surety; on whom they have been laid and borne, and who has not been spared in the least; but has borne the whole wrath and vengeance of God due to sin; and besides, though he pardons his people, yet he chastises them for their sins, and shows his fatherly displeasure at them.