Disputing jurisdiction is submitting oneself to the court, so that the court may decide the issue of jurisdiction. If you submit such a jurisdictional dispute to the court for judgement, you tacitly agree to abide by the court's judgement in the dispute.

Here, the court made such a decision, Israel is just upset they didn't prevail. If Israel didn't think the court was allowed to rule on jurisdiction, Israel would not have submitted a petition for the court to do exactly that.