The problem in this situation, in my opinion, isn't a lack of empathy, it is a fundamentally different viewpoint. Clinton doesn't see what upset Elliot because it is not a thing that would upset him, nor is it a thing he would think about being potentially upsetting, it is just too outside his reference frame. And without Elliot telling him what upset him, there is no way for Clinton to know. I honestly think that if Elliot would just tell him and explain why it was upsetting, Clinton would understand and apologise, but until Elliot learns to communicate his feelings instead of just expecting other people to read his mind, this kind of thing will keep happening.