Bases, are raid proof. People are protected for traps, sam turrets kill heli's...

But the only thing I cant figure out is that they still can kill each other?

{
  "Config Version": "1.0.3",
  "Default RuleSet": "default",
  "Configuration Options": {
    "handleDamage": true,
    "useZones": true
  },
  "Mappings": {
    "default": "default"
  },
  "Schedule": {
    "enabled": false,
    "useRealtime": false,
    "broadcast": false,
    "entries": []
  },
  "RuleSets": [{
    "name": "default",
    "enabled": true,
    "defaultAllowDamage": true,
    "flags": "HumanNPCDamage, LockedBoxesImmortal, LockedDoorsImmortal",
    "rules": [
      "anything can hurt dispensers",
      "anything can hurt players",
      "players cannot hurt players",
      "anything can hurt traps",
      "traps cannot hurt players",
      "players can hurt barricades",
      "barricades cannot hurt players",
      "highwalls cannot hurt players",
      "anything can hurt heli",
      "samsite can hurt minicopter",
      "anything can hurt npcs",
      "fire cannot hurt players",
      "anything can hurt resources"
    ]
  }],
  "Entity Groups": [{
      "name": "dispensers",
      "members": "BaseCorpse, HelicopterDebris",
      "exclusions": ""
    },
    {
      "name": "players",
      "members": "BasePlayer",
      "exclusions": ""
    },
    {
      "name": "traps",
      "members": "AutoTurret, BearTrap, FlameTurret, Landmine, GunTrap, ReactiveTarget, spikes.floor",
      "exclusions": ""
    },
    {
      "name": "samsite",
      "members": "SamSite",
      "exclusions": ""
    },
    {
      "name": "barricades",
      "members": "Barricade",
      "exclusions": ""
    },
    {
      "name": "highwalls",
      "members": "wall.external.high.stone, wall.external.high.wood, gates.external.high.wood, gates.external.high.wood",
      "exclusions": ""
    },
    {
      "name": "heli",
      "members": "BaseHelicopter",
      "exclusions": ""
    },
    {
      "name": "minicopter",
      "members": "MiniCopter, minicopter.entity",
      "exclusions": ""
    },
    {
      "name": "npcs",
      "members": "NPCPlayerApex, BradleyAPC",
      "exclusions": ""
    },
    {
      "name": "fire",
      "members": "FireBall",
      "exclusions": ""
    },
    {
      "name": "resources",
      "members": "ResourceEntity, TreeEntity, OreResourceEntity",
      "exclusions": ""
    }
  ]
}

Players can from time to time hurt each other, and cant set the sam turret to destroy heli's.

With the heli config I tried different things what where standing on this forum aswell.

Like: "players can hurt heli"

Here my config:

Please post your config in a snippet or on pastebin or similar.
I don't want to have to download an unknown file to be able to help you.

{
  "Config Version": "1.0.3",
  "Default RuleSet": "default",
  "Configuration Options": {
    "handleDamage": true,
    "useZones": true
  },
  "Mappings": {
    "default": "default",
    "dome": "exclude",
    "china": "exclude",
    "antartica": "exclude",
    "archerpvp": "exclude"
  },
  "Schedule": {
    "enabled": false,
    "useRealtime": false,
    "broadcast": false,
    "entries": []
  },
  "RuleSets": [
    {
      "name": "default",
      "enabled": true,
      "defaultAllowDamage": false,
      "flags": "AuthorizedDamage, HumanNPCDamage, LockedBoxesImmortal, LockedDoorsImmortal, ProtectedSleepers, CupboardOwnership, SelfDamage",
      "rules": [
        "players cannot hurt players",
		"players cannot hurt sam",
		"SamSite can hurt heli",
		"SamRocket can hurt heli",
        "anything can hurt dispensers",
        "anything can hurt players",
        "anything can hurt traps",
        "traps cannot hurt players",
        "players can hurt barricades",
        "barricades cannot hurt players",
        "highwalls cannot hurt players",
        "anything can hurt heli",
        "anything can hurt npcs",
        "fire cannot hurt players",
        "anything can hurt resources"
      ]
    }
  ],
  "Entity Groups": [
    {
      "name": "dispensers",
      "members": "BaseCorpse, HelicopterDebris",
      "exclusions": ""
    },
    {
      "name": "players",
      "members": "BasePlayer",
      "exclusions": ""
    },
    {
      "name": "traps",
      "members": "BearTrap, FlameTurret, Landmine, spikes.floor, guntrap, ",
      "exclusions": ""
    },
    {
      "name": "SamSite",
      "members": "SamSite",
      "exclusions": ""
    },
    {
      "name": "SamRocket",
      "members": "SamRocket",
      "exclusions": ""
    },
    {
      "name": "barricades",
      "members": "Barricade",
      "exclusions": ""
    },
    {
      "name": "highwalls",
      "members": "wall.external.high.stone, wall.external.high.wood, gates.external.high.wood, gates.external.high.wood",
      "exclusions": ""
    },
    {
      "name": "heli",
      "members": "BaseHelicopter, MiniCopter, minicopter.entity",
      "exclusions": ""
    },
    {
      "name": "npcs",
      "members": "NPCPlayerApex, BradleyAPC",
      "exclusions": ""
    },
    {
      "name": "fire",
      "members": "FireBall",
      "exclusions": ""
    },
    {
      "name": "resources",
      "members": "ResourceEntity, TreeEntity, OreResourceEntity",
      "exclusions": ""
    }
  ]
}

The config looks fine to me.
Only sugestion is to change the mappings names to ID's, I've had issues with the names translation to ID.
You say the players can hurt each other from time to time, is all over the map or single spots, and is it at a certain time or just random ?

@FuelStream I think a lot of times it would happen when in cupboard range, could that be?

I removed BaseHelicopter from this and that did the trick for the heli

 {
      "name": "heli",
      "members": "BaseHelicopter, MiniCopter, minicopter.entity",
      "exclusions": ""
    }