Question for you, how old is the controller you are using? I have noticed this issue to be more prevelant on my older worn out control as opposed to a brand new one. I have noticed that if the game registers the smallest amount of input on my right joystick then it won't let me apply Shaffer's, mods, etc... It seems to be a feature built in to prevent you accidentally scrolling across something while holding down the delete button and deleting the wrong item. When I run into this issue I check my right joy stick to make sure it is not slightly pushed up. If I make sure to reset my joy stick to a completely neutral position then I don't have this problem.
My controller is 2 months old, my old one wouldn't shoot sometimes when I pulled R2. Not sure if its lag or old controller issue so I bought a new one. Still, in crucible I will pull the trigger 3 times but it only fires twice sometimes. I'm up to 9 controllers now, cant afford to keep spending 60 every few months
Yeah I hear ya. I got a Xbox one elite controller and it was definitely more durable than the regular ones, but now after I think 3 years it's starting to show its age. My right joy stick constantly is registering an upwards input from pretty much always pushing up in video games. That's why I thought if you had an older controller it might doing the same thing as mine.