Getting a little more concrete:
Imagine a society split roughly evenly between 3 religions. Let's say 35% follow religion A, 30% follow religion B, 30% follow C, the remaining 5% belong to other religions or no religion. Approximately everyone with a religion (in our model; reality is more complicated but not sufficiently to make things inapplicable) prefers that society be organized as a theocracy according to their religion, would sufficiently accept secular tolerance, and violently opposes living under another religion's theocracy.
In this imaginary society, what is "the desire of the electorate"?
If everyone votes their honest maximal preference then the plurality says Theocracy A, which is violently opposed by 65% of the population! Picking secular tolerance over Theocracy A is not just something I (probably) prefer from the outside, but is actually preferred by the vast majority of the population over what IRV would pick!