Single 3-minute period (4 minutes for Senior major championship); Match is continuous; the three "phases" describe the techniques permitted at any given moment, not separate timed sub-rounds; Light-contact punches + kicks to permitted target areas
Why people argue about this
People often assume that since there are no knockouts allowed in JJIF's Phase 1: Striking, it means fighters can't get injured at all during these 3 minutes. But actually, what this rule does is prevent fighters from ending matches via knockout due to strikes alone; injuries and submission wins are still possible within the time limit.