Program: 57996
Project: 57996
Buggy source:
@Override public boolean onCommand(final CommandCaller caller,final String[] args){
  PlotPlayer plr=(PlotPlayer)caller.getSuperCaller();
  if (args.length != 1) {
    MainUtil.sendMessage(plr,C.COMMAND_SYNTAX,"String_Node_Str");
    return true;
  }
  final Location loc=plr.getLocation();
  final Plot plot=MainUtil.getPlot(loc);
  if (plot == null) {
    return !sendMessage(plr,C.NOT_IN_PLOT);
  }
  if ((plot == null) || !plot.hasOwner()) {
    MainUtil.sendMessage(plr,C.PLOT_UNOWNED);
    return false;
  }
  if (!plot.isOwner(plr.getUUID()) && !Permissions.hasPermission(plr,"String_Node_Str")) {
    MainUtil.sendMessage(plr,C.NO_PLOT_PERMS);
    return true;
  }
  int count=0;
switch (args[0]) {
case "String_Node_Str":
{
      ArrayList<UUID> toRemove=new ArrayList<>();
      HashSet<UUID> all=new HashSet<>();
      all.addAll(plot.getMembers());
      all.addAll(plot.getTrusted());
      all.addAll(plot.getDenied());
      for (      UUID uuid : all) {
        if (UUIDHandler.getName(uuid) == null) {
          toRemove.add(uuid);
          count++;
        }
      }
      for (      UUID uuid : toRemove) {
        plot.removeDenied(uuid);
        plot.removeTrusted(uuid);
        plot.removeMember(uuid);
      }
      break;
    }
case "String_Node_Str":
{
    ArrayList<UUID> toRemove=new ArrayList<>();
    HashSet<UUID> all=new HashSet<>();
    all.addAll(plot.getMembers());
    all.addAll(plot.getTrusted());
    all.addAll(plot.getDenied());
    for (    UUID uuid : all) {
      toRemove.add(uuid);
      count++;
    }
    for (    UUID uuid : toRemove) {
      plot.removeDenied(uuid);
      plot.removeTrusted(uuid);
      plot.removeMember(uuid);
    }
    break;
  }
default :
UUID uuid=UUIDHandler.getUUID(args[0]);
if (uuid != null) {
if (plot.getTrusted().contains(uuid)) {
  if (plot.removeTrusted(uuid)) {
    count++;
  }
}
 else if (plot.getMembers().contains(uuid)) {
  if (plot.removeMember(uuid)) {
    count++;
  }
}
 else if (plot.getDenied().contains(uuid)) {
  if (plot.removeDenied(uuid)) {
    count++;
  }
}
}
break;
}
if (count == 0) {
if (UUIDHandler.implementation instanceof SQLUUIDHandler) {
MainUtil.sendMessage(plr,C.INVALID_PLAYER_WAIT,args[0]);
}
 else {
MainUtil.sendMessage(plr,C.INVALID_PLAYER,args[0]);
}
return false;
}
 else {
MainUtil.sendMessage(plr,C.REMOVED_PLAYERS,count + "String_Node_Str");
}
return true;
}

Fixed version (ground truth):
@Override public boolean onCommand(final CommandCaller caller,final String[] args){
  PlotPlayer plr=(PlotPlayer)caller.getSuperCaller();
  if (args.length != 1) {
    MainUtil.sendMessage(plr,C.COMMAND_SYNTAX,"String_Node_Str");
    return true;
  }
  final Location loc=plr.getLocation();
  final Plot plot=MainUtil.getPlot(loc);
  if (plot == null) {
    return !sendMessage(plr,C.NOT_IN_PLOT);
  }
  if ((plot == null) || !plot.hasOwner()) {
    MainUtil.sendMessage(plr,C.PLOT_UNOWNED);
    return false;
  }
  if (!plot.isOwner(plr.getUUID()) && !Permissions.hasPermission(plr,"String_Node_Str")) {
    MainUtil.sendMessage(plr,C.NO_PLOT_PERMS);
    return true;
  }
  int count=0;
switch (args[0]) {
case "String_Node_Str":
{
      ArrayList<UUID> toRemove=new ArrayList<>();
      HashSet<UUID> all=new HashSet<>();
      all.addAll(plot.getMembers());
      all.addAll(plot.getTrusted());
      all.addAll(plot.getDenied());
      for (      UUID uuid : all) {
        if (UUIDHandler.getName(uuid) == null) {
          toRemove.add(uuid);
          count++;
        }
      }
      for (      UUID uuid : toRemove) {
        plot.removeDenied(uuid);
        plot.removeTrusted(uuid);
        plot.removeMember(uuid);
      }
      break;
    }
case "String_Node_Str":
{
    ArrayList<UUID> toRemove=new ArrayList<>();
    HashSet<UUID> all=new HashSet<>();
    all.addAll(plot.getMembers());
    all.addAll(plot.getTrusted());
    all.addAll(plot.getDenied());
    for (    UUID uuid : all) {
      toRemove.add(uuid);
      count++;
    }
    for (    UUID uuid : toRemove) {
      plot.removeDenied(uuid);
      plot.removeTrusted(uuid);
      plot.removeMember(uuid);
    }
    break;
  }
default :
UUID uuid=UUIDHandler.getUUID(args[0],null);
if (uuid != null) {
if (plot.getTrusted().contains(uuid)) {
  if (plot.removeTrusted(uuid)) {
    count++;
  }
}
 else if (plot.getMembers().contains(uuid)) {
  if (plot.removeMember(uuid)) {
    count++;
  }
}
 else if (plot.getDenied().contains(uuid)) {
  if (plot.removeDenied(uuid)) {
    count++;
  }
}
}
break;
}
if (count == 0) {
if (UUIDHandler.implementation instanceof SQLUUIDHandler) {
MainUtil.sendMessage(plr,C.INVALID_PLAYER_WAIT,args[0]);
}
 else {
MainUtil.sendMessage(plr,C.INVALID_PLAYER,args[0]);
}
return false;
}
 else {
MainUtil.sendMessage(plr,C.REMOVED_PLAYERS,count + "String_Node_Str");
}
return true;
}