You're right. I think for the most part, I missed it because there the mission involved and I think stepping into the Chief's shoes, when he was worried, he also had a mission to bring Cortana back to Halsey, he had an objective to follow. His actions and lines shows concern and also still hope to get Cortana fixed.. in the ending however, there isn't a mission left for him. And he's just getting hit with all this emotion all at the same time. When he was on the flight deck later, starting off into space, if Spartans ever had an emotional wreck phase, that was probably all we'll get.