This may not be an issue for everyone's gamepad, but it is for mine.
Anyway, the problem is that when pressing X to customize a radial hotbar button, as soon as the context menu opens it will immediately begin scrolling through it because the control for the context menu, the Left Stick, is still tilted.
I thought I found a way to fix it but it actually only works about 75% of the time..
temporarily disabling the joystick seemed to work if I did so just slightly after pressing the X button, but apparently the timing is inconsistent.
I guess this post should instead go into the bug reports. Thanks