### Preflight Checklist
* [x] I have read the [Contributing Guidelines](https://github.com/electron/electron/blob/master/CONTRIBUTING.md) for this project.
* [x] I agree to follow the [Code of Conduct](https://github.com/electron/electron/blob/master/CODE_OF_CONDUCT.md) that this project adheres to.
* [x] I have searched the issue tracker for an issue that matches the one I want to file, without success.

### Issue Details

* **Electron Version:**
  5.0.1
* **Operating System:**
  windows
* **Last Known Working Electron version:**
  n/a

### Expected Behavior
A preload script should run only 1 time for each webContents / iframe

### Actual Behavior
The preload script appears to run multiple times

### To Reproduce
https://github.com/Tim91084/electron-node-subframe-issue/tree/node-in-subframe-runs-too-often

```sh
$ git clone https://github.com/Tim91084/electron-node-subframe-issue.git -b node-in-subframe-runs-too-often
$ npm install
$ npm start || electron .
```

### Screenshots
![image](https://user-images.githubusercontent.com/5086428/58273769-63b9d900-7d5f-11e9-8d30-1525dea34ce3.png)

shell/renderer/atom_sandboxed_renderer_client.cc
content::RenderView* render_view) {
  RendererClientBase::RenderViewCreated(render_view);
}
void AtomSandboxedRendererClient::RunScriptsAtDocumentStart(
    content::RenderFrame* render_frame) {
  if (injected_frames_.find(render_frame) == injected_frames_.end())
    return;
  auto* isolate = blink::MainThreadIsolate();
  v8::HandleScope handle_scope(isolate);
  v8::Local<v8::Context> context =
      GetContext(render_frame->GetWebFrame(), isolate);
  v8::Context::Scope context_scope(context);
  InvokeHiddenCallback(context, kLifecycleKey, "onDocumentStart");
}
void AtomSandboxedRendererClient::RunScriptsAtDocumentEnd(
    content::RenderFrame* render_frame) {
  if (injected_frames_.find(render_frame) == injected_frames_.end())
    return;
  auto* isolate = blink::MainThreadIsolate();
  v8::HandleScope handle_scope(isolate);
  v8::Local<v8::Context> context =
      GetContext(render_frame->GetWebFrame(), isolate);
  v8::Context::Scope context_scope(context);
  InvokeHiddenCallback(context, kLifecycleKey, "onDocumentEnd");
}
void AtomSandboxedRendererClient::DidCreateScriptContext(