There's always a possibility of being denied entry, even at first entry. An example of how this might happen is if one were to write "4 months" as the "intended length of stay" on the landing form and when told by the immigration officer that the limit is 90 days, responding with "I know that, but I plan to make an overnight trip to Korea midway through to restart the 90-day clock."

Even though the side trip method usually works in practice and many people do it, declaring it up front would probably not be a good idea. That said, the chances of a US citizen being denied entry on the way back from a short Korea side trip are rather small, especially the first time it happens. I've heard of it being a problem for people that keep it up for the better part of a year.