Stubbs says the following just before clearing "Charlotte":
You know, the old man himself hired me.
So many years ago I can barely remember it.
But he was very clear about my role here.
About who I was supposed to be loyal to.
I guess you could call it my core drive.
And this project the company started blurs the lines.
You know? I'm just not sure who you're supposed to be loyal to in a world like that.
But what do I know? Guess I just stick to the role Ford gave me.
I'm responsible for every host inside the park.
Interpret this how you will, but I took this to mean that Delores didn't pass the scanner's test, but Stubbs chose to let her pass anyway. If she's out of the park, she's not his responsibility.