Jephthah’s victory over Ammon had meant he must fulfill his vow and sacrifice his daughter. The actual fulfilling of that vow would be two months later, to give his daughter time in the mountains with her friends to weep and mourn (Judges 11:38). So this conflict at the start of chapter 12 likely happened in the meantime. Ephraim likely did not wait two months after the victory before going across the Jordan to complain to Jephthah.
1 The men of Ephraim were called to arms, and they crossed to Zaphon and said to Jephthah, “Why did you cross over to fight against the Ammonites and did not call us to go with you? We will burn your house over you with fire.”