I'm using an XBOne controller on OS X Catalina (i heard people on windows also have this problem sometimes). Every minute or two the keys suddenly stop responding until I pause-unpause the game. Please don't tell me to turn on native controller support (i have already done this and without that setting the game doesn't respond to the controller at all) EDIT: none of the answers below actually helped.
Hollow Knight seems to have an issue with Xbox controllers in general. I've done some research and found the following articles:
Right click steam and open up "big picture". Once there, click the "gear" in the top right. Open up controller options, and enable xbox 360 configurations. Unplug your controller after you've saved it, and you're ready to go!* - This seemed to work for many people.
I quit the game, opened Steam Big Picture mode, DISABLED the Xbox controller configuration and then quit Big Picture mode. The controls in HK were just about perfect and how I remember them from a week ago. I then turned OFF v-sync and that improved things even more.* - The issue was that buttons kept on triggering repeatedly
enable "generic controller support" in settings then define layout, and you should be good to go* - This was from someone using an Xbox 360 controller emulator.