Input from controllers not being read after a while

I have an iPad air 2 on iOS 10.3.3 non-jailbroken. I have an issue where after a while (could be 20-60 mins) the inputs from my controller are not being read. The controller remains connected to the ipad and will work if I try it with another app/game. But I have to wait maybe about 30 seconds for it to start working again in retroarch. It has happened on multiple different cores. I have tried with both of my controllers (SFC30 and FC30 PRO from 8bitdo) and it happens to both of them. I have not had any issues with these controllers on windows/android versions of retroarch. Thank you in advance for any help.