Contradiction with 1 Samuel 6:5
While Exodus 8:31 speaks of the Lord removing the flies completely at Moses' request, 1 Samuel 6:5 implies people should make offerings for afflictions rather than just asking for their removal.
1 Samuel 6:5: Wherefore ye shall make images of your emerods, and images of your mice that mar the land; and ye shall give glory unto the God of Israel: peradventure he will lighten his hand from off you, and from off your gods, and from off your land.
Contradiction with Jonah 3:10
Jonah 3:10 describes God seeing the people's repentance and choosing not to bring destruction, contrasting with Exodus 8:31 where God's action seems more direct in response to a plea without requiring repentance.
Jonah 3:10: And God saw their works, that they turned from their evil way; and God repented of the evil, that he had said that he would do unto them; and he did [it] not.