with extend_prototypes false

controllers.application.js

import Ember from 'ember';

export default Ember.Controller.extend({
  appName: 'Ember Twiddle',
  
  errors: null,
  
  init() {
    this._super(...arguments);
    
		let errors = Ember.A();
  	errors.pushObject({
      'code': 140,
      'message': 'Hello World'
    });
    this.set('errors', errors)
	},
  
  actions: {
  	clearErrors() {
    	this.get('errors').clear();
    },
    consoleLogClear(){
    	console.log(this.get('errors').clear);
    }
  }
});

templates.application.hbs

{{errors.firstObject.message}}
<button {{action "clearErrors"}}>Clear errors</button>
<button {{action "consoleLogClear"}}>Output the .clear function to console</button>

twiddle.json

{
  "version": "0.11.0",
  "EmberENV": {
    "EXTEND_PROTOTYPES": false,
    "FEATURES": {}
  },
  "options": {
    "use_pods": false,
    "enable-testing": false
  },
  "dependencies": {
    "jquery": "https://cdnjs.cloudflare.com/ajax/libs/jquery/1.11.3/jquery.js",
    "ember": "release",
    "ember-data": "2.11.0",
    "ember-template-compiler": "release",
    "ember-testing": "release",
    "prototype": "https://ajax.googleapis.com/ajax/libs/prototype/1.7.3.0/prototype.js"
  },
  "addons": {}
}