The Lord granted the Benjamites success to discipline the other Israelites for their independence, not because He approved of the Benjamites' actions. The Benjamites became God's temporary instrument to discipline the other tribes, as God also used Israel's foreign foes (the Canaanites, Midianites, Philistines, et al.).
"The congregation now discovered, from this repeated defeat, that the Lord had withdrawn His grace, and was punishing them. Their sin, however, did not consist in the fact that they had begun the war itself--for the law in Deut. xxii 22, to which they themselves had referred in ver. 13, really required this,--but rather in the state of mind with which they had entered upon the war, their strong self-consciousness, and great confidence in their own might and power. They had indeed inquired of God (Elohim) who should open the conflict; but they had neglected to humble themselves before Jehovah the covenant God, in the consciousness not only of their own weakness and sinfulness, but also of grief at the moral corruption of their brother tribe."363
With each successive defeat the Israelites became more concerned about getting God's guidance. They had previously just asked Him to bless their plans with success.
". . . by reducing the size of the army, God was showing them that numbers alone did not guarantee victory. They needed to trust God to accomplish the impossible, as he did for Gideon's three hundred (cf. 7:7)."364
"Just as the worship of Baal had brought about a near catastrophe in the plains of Moab (Num 25:1-9), so the Baal cult was probably responsible for subverting the Benjamites. This must have been comparatively soon after the earlier incident, for the same priest Phinehas intervened on both occasions (Num 25:7-8; Judg 20:28)."365