Yea, like when I am selling items there is no way to keep that Confirm/Y as a single consistent button. Or when you loot, sometimes it indicates you need to Hold or Press the button and if you remap it then displays the remapped button but only the original binding works- the phone calls also are like this.
Pick up the body with R, but drop it with E.
There were some vehicle controls as well I do not remember that functioned in a nonintuitive manner for me- but I just stopped messing with them altogether out of frustration. And so on.