I use Keyboard + Mouse on PC but each time I load a savegame or start the game, I get this popup saying mouse detected, controller settings adjusted or so.

Any way to stop that? I notice it also prevents me from performing any action after loading a save for several seconds

Same for me. It is quite annoying but I started to "filter" that in my brain :) But it does not prevent me from doing anything, just popping up in the lower left corner.