I just purchased an Xbox series s and a second ms controller. I was able to sync the controller and both work on the main Xbox screen and sub pages. However, when I go into a game (Injustice 2 or MK11) the second controller will not work. I have even been able to swap controllers but only one works at a time in the games. Any help will be much appreciated.
Are you launching the controller as a different user or the same user?
I have tried using my profile. And I also created a second profile and assigning it.
First of all welcome to the community. 
If any problems occur, I would do a hard reset. Hold the power button at your console for about 10 seconds. After that turn it back on.
You could also try to update your controller.
And the last thing would be to unplugged the console for 15mins, plug it back and try if it works.
There could also be some problems if you are part of the insider program.
EDIT: I would also try a different game. MK and Injustice are from the same developer and publisher.
I’ve done the hard reset and updated everything. I’ll try the unplugging after work today. Thank you