Every time you try to enter the controls in the option the game crashes and you get the following error:
The Following Error has occurred

Generic Game Error

ASSERTION: 'i < NUM_OPTIONS' at C:\projects\tomb raider\Game\frontend\menu.c(231)

The game simply doesn't know how to handle some devices. Or at least that's my guess.
It doesn't matter if you have the device enabled or disabled in the settings. As long as it will show up on the list in-game, it will crash the game.

1. Unplug one USB-Device from your computer
   
2. Start the game and go into controls.
   
3. Now, a couple of things can happen
   
   • If the game crashes again with the same error message, unplug another device (might be more than one that causes this) and go back to step 1.
     
   • If you now can enter the controls settings. Plug back in the other USB-devices and try again.
4. If you need the device that causes the crash, try to find some older kind of it (or if it's not a controller, change the controls when the device is not plugged in)

In my case the crash was caused by my headset, so I found an old 3.5mm headphones and the game hasn't crashed since. Though the error message still comes up after I exit the game.
This had a nice bonus effect of fixing the audio so it didn't become static every time I made a load :)