Yeah, Jean is definitely looking at Armin, with one eyebrow raised. He hasn't forgotten the talk he and Armin had, a long time ago, about Armin's suspicions regarding Annie. But then Annie had showed up in this world, and Armin hadn't said a word about her. Jean knows Armin well enough to imagine he'd confronted Annie, and since he's said nothing to Jean, Jean assumes that nothing came of that conversation, and that Armin's reaction is probably embarrassment.

Well. Armin did always act like he had a bit of a crush on her.

"Annie's pretty capable. The most capable out of all of us, really." Jean turns back to Marco. "But you're taking Polo with you. Team Rocket has been quiet lately, but I don't want any of your Pokemon getting stolen by them."