Albert Barnes Commentary Judges 12:4

"Then Jephthah gathered together all the men of Gilead, and fought with Ephraim; and the men of Gilead smote Ephraim, because they said, Ye are fugitives of Ephraim, ye Gileadites, in the midst of Ephraim, [and] in the midst of Manasseh." — Judges 12:4 (ASV)

Because they said ... - This passage is extremely obscure. It can be rendered as follows: The men of Gilead struck Ephraim, because they (the Gileadites) said, 'You are the fugitives of Ephraim.' (Gilead lies between Ephraim and Manasseh; and Gilead took the fords of Jordan before Ephraim. And it happened, when the fugitives of Ephraim said, 'Let me cross over,' and the Gileadites asked him, 'Are you an Ephraimite?' and he answered, 'No,' then (the Gileadites) said to him, 'Say Shibboleth,' and so on. So they (the Gileadites) killed them at the fords of Jordan).

Everything within the parenthesis explains the brief statement, “They struck them, because they said, ‘You are the fugitives of Ephraim;’” That is, in spite of their denial, the Gileadites determined that they were the fugitives of Ephraim and so pitilessly slaughtered them when they attempted to return to their own country through Gilead.

This part of Gilead, where the fords were, was clearly not in Manasseh, but in Gad. The word “Slew” (Judges 12:6) implies “slaughtering” in cold blood, not killing in battle .

The word in the original text is the proper word for slaying animals for sacrifice.