Alyssa being the only other girl besides Charlie and Theresa.. til scorch trials of course.
that being said Alyssa is in love with Thomas, he utterly loves her too, he's just more concerned with keeping everyone alive as of right now but he is not showing that too much.
Thomas happened look around for her, when he couldn't find her, he panicked because he loved her and because that's his best friend's little sister, he didn't like that he lost her during this time.
"ALYSSA!!!!" He began running around, Newt followed Because he is worried about her too.
"shit.. did we lose Alec's sister while he's asleep?"
"MHM! YES NEWT" Thomas was panicking but then he saw her, he hugged her "Oh thank you.. don't do that to me again..."