Surely this seems like a subjective question but it seems to me that all the counterexamples against utilitarianism are just designed to move the problem when we can't really judge it.
For example the Trolley problem shows us the clear example when we have a single leaver to make a decision. But in case of pushing a fat man over the bridge to save five people, the situation is designed so that the there is a hidden negative variable in the utilitirianistic option: The pain of the fat man, the pain of you as the murderer and the extra pain of the workers in case you screw up your mission (which sound very realistic). (I think everyone would agree that killing the fat man in the Trolley problem is not a* bad thing* to do even though they wouldn't do it themselves.)
The same goes for the example with saving someone using organs of 5 other people or eradicating a 6-million inhabitants planet instead of a 12-million one. Some people give as an example the philosophy of nazism - in this case I think we can consider the contempt of persecution of minorities/diseased as a sort of social contract).
So could there be a situation when the total happiness of one option is less than the total happines of another and yet, it would cause more "harm"?
In other words, what else should we consider in our choice apart from the "overall happiness" whatever it is?