I've had this bug since day one the game came out. Originally started on the OG Xbox one, now on the X One X. Anytime the controller dies disconnects from the cord I get the menu pop up on the screen, doesn't matter if it's menus or in game. Cannot dismiss the pop up no matter what. But I'm still in control in the game i e: I can still move around access in-game menus but the pop-up is still on screen and does not disappear unless I restart the game by closing it out and restarting. Everything I have ever done to try and get rid of it has not worked and the only workaround I have found is to make sure that my controller is charged before I start playing.
I've had this issue since day 1 of the game. Doesn't matter where, when or the circumstances of the disconnect. The only fix immediately I found effective is to reset the game, which obviously can be catastrophic in game. So the only thing I recommend, which I do is make sure either that the controller is plugged in charging while playing or make sure your controller is charged before playing.