It's hard to say with this game, in any other I would say something broke in updating from 0.061 to 0.062. Last I saw Isabella she asked if we wished she were more like Nanami, asked if we'd still love her if she couldn't be like that (I say yes twice), then demands we keep Nanami out of the house. We refuse (no choice, possibly due to previous choices) and she throws a fit and runs out.
The next scene we're meeting her in a coffee shop and MC has a vast number of options on how to apologize. Apologize for what? I feel like I've missed a scene, and there is literally zero context provided in their conversation for what they're talking about. Are we sorry we didn't give in to her demands? Sorry we've been a terrible father? MC says he "didn't mean those words" and Isabella "can't believe you said those things to me". That has nothing to do with how the last scene played out.
There's been many times in this game I can't follow the dialogue, it veers wildly from philosophical musings to angry overreactions seemingly at random. But this was the first time an entire scene left me so bewildered that I felt it might be a bug.