It seems that if emotions are going to be rational, then the best explanation of this will have to be that they are rational in virtue of the rationality of the beliefs included in the emotion. Why is it irrational to get angry that there is an odd number of pebbles in the fishbowl? Because it’s irrational to believe that this is a bad states of affairs. Why is it rational to get angry at someone who steals money from you? Because you’re rational in believing that this is a bad state of affairs.
One quick point: the cognitive components of emotions are not properly 'beliefs' -- they might even conflict with our beliefs. But I agree with the broader point that cognitive misjudgment is one common source of irrationality in emotion. Might there also be others, though? Justin Oakley argues that emotions are complexes of cognition, affect, and desire; it seems to me that there may be rational failings in respect of all three.
Consider someone who is disproportionately angry about some minor wrongdoing. Their judgment of wrongdoing seems accurate enough;* the problem is instead an excess of affect. The excessively angry agent obsesses over this one problem, to the detriment of more pressing issues. For another example:
Good things generally warrant positive reactions. But envy consists precisely in feeling bad or resentful about the good things that happen to other people. Doesn't that just seem fundamentally misguided? Similarly for schadenfreude, or taking pleasure in others' suffering. It's simply perverse; not an apt response to the normative features of the situation.
Moreover, jealousy may involve a desire for the target to lose the benefit you so resent them for. But it is generally irrational to desire a Pareto loss -- for someone to be harmed and nobody to benefit. So jealousy and the like are irrational for this reason too.
* Now, it may be claimed that the desirous and affective components of emotions should also be incorporated into their cognitive component, in the form of normative claims. Maybe envy doesn't just consist in judging another to have benefited and feeling negative affect about this; perhaps we could say it also involves an implicit judgment that it is bad that the target benefited so. To the jealous desire we might add a judgment that it would be right to deprive them of this benefit. And so on. But if we build everything into the cognitive component to begin with, then it's trivial that it will suffice for all aspects of rational evaluation. So I think the substantive point to note here is that affect and desire are open to rational assessment too, even if they are ultimately incorporated into the cognitive component of emotion.
Incidentally, this proposed melding of cognitive and non-cognitive components of emotion relates to my earlier comments about 'rich' or interpreted phenomenology. Perhaps the broader lesson is that these enriched "components" are not really distinct and independent components at all, but instead draw our attention to a single (conceptually inextricable) state that may be variously described as a kind of judgment, a kind of desire, or a kind of phenomenal affect or 'feel'. Really what it is is just one thing, an affectively motivating intentional state, i.e., an emotion.