You could try highlighting the controls that being modified. There should be a highlight method on web controls. There's no way to automatically do it though as far I know. You'd have to call it each time you perform an action on a field.
We inject extra text fields and drop downs into some of our web applications. We experimented with making the injected controls a different color to signify the controls are not a part of the native application. However, people eventually forgot about the colors. When people aren't using our automation tools, we now get complaints that buttons are missing from the applications.
If you just want to make a small note for troubleshooting purposes, it might not be too intrusive to add extra text at the bottom of the page. "Page modified by Pega Robotics."