yes of course, but even then we are left to describe such intransitivities in a useful manner rather than conclude the actors is simply non-rational.
If it were so, then human behavior would be impossible to analyze. Instead, if we focus on causes and consequences of non transitive preferences - like in behavioral economics - we may regain the ability to do analyzes.
Preference relations of rational agents are, anyway. When it comes to us mere mortals, well, see https://en.wikipedia.org/wiki/Intransitivity#Occurrences_in_....