Factorio Forums

As you can see these are mod-related controls, unsure if it can happen with the vanilla ones. Anyway, what happened is I right-clicked some of the commands to unset them, because I didn't plan on using them and didn't want to activate them by mistake or worry about conflicts. Initially it seemed to work as expected, but after restarting the game, it shows "Not set" but with the modifier key it used to have. As far as I can tell it has no actual effect on the game, but even if it's only visual it's a little disconcerting.

Thanks for the report. It's now fixed for the next version of 0.16.