One of the few times Spock was not logical was when she chose the other Vulcan over Spock. Spock knew she had made the logical choice but he told her that sometimes what is logical does not turn out to be what is best or words to that effect.
Spock was probably ticked off because the other Vulcan looked like Gilligan.
He’s actually addressing Stonn, the rival:
Stonn, she is yours. After a time, you may find that having is not so pleasing a thing after all as wanting. It is not logical, but it is often true.