I do not understand this question. What is the set which is ordered and what is the relation on that set that you are talking about? It seems that you want to order states of a state transition system which is typically not done.
If so, yes, then reflexivity would be a self-loop. But usually transitivity is not given (and you would have to consider reachability instead), and most of all, you could not have any cycle in the transition system which means that if a program is modeled, it could not have any loop. So, what I want to say is that transition systems that model systems are typically not representing orders.