That sounds like a raid engine. If a system with a raid engine goes on alert (large fleet in an adjacent system or a command center in an adjacent system is destroyed), they'll send waves to that system every 3 minutes. The ships SHOULD go after you (they might wait around for friends but they should eventually become aggressive), but I've had similar cases where ships that become threat aren't really interested in going anywhere. It might be a bug, if you posted a save file someone might be able to figure out if those ships are behaving correctly.