there are quite a few way of saying this but really the undertone is troublesome, or disturbing in some way

To take "subtext" first, I think it more specific than an undertone; it's an implicit message. Interrupting someone is a way of saying to them "what you have to say is not worth listening to", without actually saying it.

"Poignant" is tricky, because it most often means evoking feelings of sadness or regret (the only meaning given in some dictionaries), but it clearly doesn't mean that here. Nor, in my opinion, is the meaning precisely distressing or painful, though that's debatable, and the effect of being interrupted, with its subtext, can no doubt have that effect. I think it means sharp and pointed, the meaning it has in "poignant wit" or "poignant satire" or "poignant criticism", which reflects its etymology (from pungere, 'prick, pierce'). So I think your own suggestion of "cutting" is actually as close as you can get. In other words, I think it refers to the nature of this kind of passive aggression from the perspective of the perpetrator, rather than the victim.

"Something that is poignant "pierces" the heart, senses, or emotions. You will see poignant used three different ways: Something that is emotionally touching or painfully sad can be described as poignant, like a poignant scene in a movie; secondly, it can mean biting, acute, sharp, or piercing, like a poignant critique or a person's poignant wit; finally, it can be used to describe something that sharply affects the senses, like a poignant odor or poignant beauty."
http://vocabulary-vocabulary.com/dictionary/poignant.php