Throughout the game i have noticed many weird examples of where doing something that some people would consider good gives you dark side points and the opposite for light side points. One example i will use is early on in the troopers story he is given a choice of giving the medicine to republic soldiers or refugees who stole the medicine from the republic. I opted to try and give the medicine back to the republic since they are the ones who are protecting the refugees but when i chose that it will give you 100 dark side points. I think many situations in the game would have been better if they didnt effect your light/dark allignment overall since they are too grey.