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Because:

• you overwrite existing implementations (like in your example)
• that implementations influence the global behavior (no encapsulation)
• modified behavior can harm 3rd party modules behavior
• you can generate instability and vulnerabilities

But it is OK to use polyfills (and add-ons) like that:

if (!('entries' in Object)) {
  Object.defineProperty(Object, 'entries', {
    value: function(obj) {
      return Object.keys(obj).map(function(key) {return [key, obj[key]]})
    }
  })
}

PS: Sorry, entries is not defined on Object.prototype, but you know what I mean.