Not Wrong, but Other.
Didn't you say there Was an affair after all? That is both cause for, and a direct consequence of, insecurity in the relationship. What the cards may have been wanting to tell the seeker the truth about the seekers partners insecurity and doubt. What the seeker in turn chose to do with that information is her matter. And even though the partner didn't agree that it was the affair that caused the relationship to end, I find it next to impossible to believe that it had no effect. It's not like you have an affair if you are 100% satisfied with your relationship. And having sex, or even just going out with someone, has an effect on your emotion, causing you to either like, or dislike the person more. Liking the person your cheating with reduces your attention for your current "official" partner, and thus causes further instability. Disliking the person you're cheating with (which is also a posibility) causes you to be ucomfortable with the affair itself, and that discomfort will spread to your "official" relationship.
So the cards were evidently reading, as a fellow forumist said, a universal truth. You read one aspect of it, communicated that information to the querrent, and it was shown to be the case of the situation. The querrent may disagree with the cards, but she can't deny that what they objectively said is true.
On the other hand, if I misunderstood you completely on that last sentence, and there was no affair, if you were to look through the reading again, Would you not find another, at least simular way, of reading the cards. They might speak of insecurity, separation, isolation, jealousy, or disatisfaction. I would possibly, as a reader, translate this into english as that it is likely that the cards are trying to say that there is an affair going on between your spouse and another, but it is also possible that the cards were telling of the situation between the two, and that there is enough problems that one of the partners may be at risk of being unfaithful, (or if he/she has got any form of dignity, simply break up) but have not yet taken action.
This alll comes with experience. I am personally relatively inexperienced with the arcana, and have made simular mistakes myself, but my experience with people, and my experience with putting situations together, understanding how circumstances reflect on each other, and understanding the result of an event or situation, has been of much use to me. The tarot is, to me, simply a way to determine what exactly the case is, what the question is about. They are advisors, sugestors, not eyes. They read people, usually feelings or traits, but rarely actual situations or events (though exceptions occur in every carft and plain).
Sorry for the long, and probably rather incomprehendable and barrock answer, but I hope you understand what it is I am talking about anyway.
Blessed be.
EDIT: What exacly did she mean when she said that was not the reason? Did she know for a fact? If so, did she know other things that supposedly wasn't the reason? If so, couldn't she have, in the same way, found out on her own what the real reason was?