I had the same issue on our third person local co-op shooter game and I've burned countless hours only to conclude that it's bugged. I recommend ditching Unity's InputManager and use XInputDotNet (https://github.com/speps/XInputDotNet). Using this lib instead fixed all the issues I had with multiple controllers and trigger buttons. One caveat: it's not going to work on the OSX. As an alternative, you can then try XBoxICtrlrInputXBoxCtrlrInput lib. It boasts OSX support but I can't fully vouch for it as I've only used it briefly (https://github.com/JISyed/Unity-XboxCtrlrInput).