For some reason people often refer generally to men by their last name. There is no particular reason for it and it is not as a rule meant to be either endearing or affectionate. It is mearly used as a substitute for the first name. However in this case it has a lot to do with a follow the leader syndrome started by Dr. Brennean who was trying to be as impersonal as she could be following their first meeting at the airport where she was held after putting the hurt on a Homeland Security guy who was trying to hold her for Seely. Everyone just played follow the leader after that when they heard her use the name.
My evaluation of your question. Hope it helps.

Hodgins is also called 'Jack' by some people. But I agree with Councilman.