It's a tool but it's not a strict computer program, and the language we use for computer programs doesn't capture their behavior well. In squishier fields like bio, where model organisms are used as living protein factories, there's a reason we don't call maladaptive behavior a bug. When dealing with useful but complicated black-box systems, we should feel free to reach for any metaphor we please.

Would it make you feel better if the user said 'It'll make significant changes to how the code works. In the COT, it brings up explanations that resemble anxiety about copying code, and my suspicion is that this is the proximal cause of the changes it's making.' -- this is inarguably true, and very likely what the guy you're responding to meant.