“I’m sorry you misunderstood what I said and got upset!”
Ever felt like saying that to your bride? You said something, she heard something that was not there (really, really was not there) and got upset. Even if she believes you didn’t mean what she read into it, she’s still hurt. You want to apologise, but for what? For her past, that causes her to hear something someone else said that you don’t even think? On the other hand, you don’t want to imply you were at fault because that would be dishonest.
How about “I’m sorry what I said hurt you – what I meant was …”
Or maybe even better: “I can see how you would have thought I meant [whatever], I’m sorry my words hurt you. Let me try again.”