That wasn't the only time they were not alone. Before Luke had reconnected with the Force, Kylo and Rey were talking to each other outside of her hut. Luke had no idea that Kylo was there, even though he was watching Rey as she was talking to him. And Kylo couldn't see Luke because he was following Rey's eyes when she turned to Luke and had to ask her if it was Luke she was turning to see. Also, the caregiver nuns were cleaning debris the whole time right where Rey was seeing Kylo. They didn't see him there either.
After Luke reconnected with the Force, that's when he was aware of what Rey was doing when she was touching Kylo's hand in the hut. And even then, it's not clear if Luke saw Kylo, or was just aware of what he perceived was happening in Rey's mind. When Rey turned toward Luke, Kylo instinctively turned to what she was looking at. The Force Skype stuff was *not* projection.
What Luke did on Crait was entirely different. Kylo was aware of Force projection (probably learned it from Master Luke), because he questioned whether Rey was projecting herself to his star destroyer. He concluded that: "You're not doing this. The effort would kill you. This is something else." That was when we the audience were told two things explicitly that would crystallize later: 1.) Kylo and Rey were not Force projecting, and 2.) Force projecting requires effort that kills the user.