I'm not sure why anyone would get upset if there's no intent of malice. That just doesn't make any sense.
Well for one it's not always easy to determine what is or isn't malice, secondly, neglect or inconsiderate behaviour can also be upsetting. When you're emotionally vulnerable and the other party just kind of jokes about a sensitive issue, you start to wonder how much they care, whether they know what makes you tick, how they could hurt you so when you've opened up etc.
I'm not saying INTJs are always justified in being upset, in fact we can get explosively upset at very tiny things that crack our shells and be overly let down when people don't take them *seriously*. From experience with my brother, he will foreground an issue and joke about it whereas my father will pick up on my gravitas and join me in my dejection, awkwardness, treat it with respect. Sometimes the joking is actually good for me, but all in all it seems preferable that someone understands the whys and hows of your emotional states. That said if she broke up with you, it's more likely to be about a pattern than one thing you did. It may have counted as a final confirmation that the way you are, the way you deal with emotions wasn't compatible with hers. She may have been overdramatic in that state. So what upset her probably wasn't the remark itself, but what the remark said (or what she interpreted it as saying and feelings can warp our powers of interpretation) about how you related to her/your relationship.
Unfortunately we don't always let people know we're assessing that stuff, because we think people should be whoever they truly are, because we want to observe that and decide accordingly. A point of view which has its limits and, well, isn't great for communication. And I think we can get pretty moody.