I confirm it's not a bug and there's nothing to fix, except maybe just the wording of the message, so you won't be confused thinking you have to acknowledge that message, when you don't.
That message is just something to get your attention ( in Beta, it used to say "1, 2, 3 - headphones check" ), you are not supposed to reply to it. In fact, if you press CTRL+F12 and read the window Title, is saying "Cancel pushback ?" so the Yes/No question refers to the cancellation, and if fact it's exactly what it does, if you select Yes, the Pushback is canceled.
We'll change the message with something like "Captain, this is ground crew, we are ready for pushback" so it would be more clear it's not a question you are supposed to answer.