When Stubbs stopped the Dolores-as-Charlotte host on her way to the boat to the mainland, he says Ford hired him "so many years ago I can hardly remember it". This sounds an awful lot like Bernard, back in Season 1, before anyone knew he was a host. He also says "he (Ford) was very clear about my role here, who I was supposed to be loyal to. Guess you could call it my core drive." Is he really a host?
This is was co-creator Lisa Joy had to say about it:
When Halores left the beach, it seemed like Stubbs knew it was Dolores — or at least that it wasn’t Hale. Is that safe to assume?
Yes! It is safe to assume. And there is a step further that you can assume too. And we don’t say it explicitly, but if you are left wondering with all [Stubbs’] talk, his knowing talk about, “I’ve been at the park a very long time,” and Ford designed him with certain core drives, and he’s gonna stick to the role he’s been programmed with; it’s a little acknowledgement of just why he might have his suspicions about what’s going on with Hale, and then lets her pass.
And doesn’t it make sense if you are Ford and designing a park and you have a whole master plan about helping robots that you would keep one Host hiding in plain sight as a fail-safe? Maybe the Host who’s in charge of quality assurance? And by the way, that was totally meant to be subtle [laughs].
Fred Toye, the director of the episode also confirmed that, as far as he knows, Stubbs is a host (and the scene was re-written by co-creator Jonah Nolan the night before it was shot)