Some cutscenes can make no sense depending on your morality route, for example you can directly disobey and betray Black Doom but the next cutscene acts like Shadow never betrayed him at all and has always been loyal to him.
The G.U.N commander blames shadow for the ARK raid and has held a grudge for revenge for 50 years, despite being on-board as a child at the time of the raid, so he should know that G.U.N killed everyone. What is most puzzling about this is that he now works for the organization that ruined his life.