I also have the same condition with the Pi 3B+ and NESPi+ case running most recent RetroPie 4.4 release. It seems to happen with all wireless dongles connected in to the NESPi case ports (wireless Keyboard, and Xbox 360 adapter for sure). I found a couple different threads in the forum about it and I believe they found the reason, https://github.com/raspberrypi/linux/issues/2408, and I believe they were working on a fix, but I have not seen the true fix anywhere.
(If anyone has it and a step-by-step, I'd be grateful)
**I did find a temporary workaround though, without having to revert to previous Pi versions-
Use another USB hub (like a laptop 4-port) to connect to the NESPi case, and then connect your devices in to that. It appears to cancel out whatever mismatch there is between the pi and NESPi USB hub.
It's a bit unsightful but it prevents a lot of re-imaging and reversion to a previous release. Hopefully a solution will be embedded in to the next release as the NESPi case is great!
*I have been successful using either an Insignia 4 port USB2.0 Hub (N5-PCH5420) and also with a Sabrent 4 port USB3.0 Hub (HB-MNBW). Not sure if a powered USB hub will do the same but worth a try before frustrating yourself to no avail looking for a solution.
My devices connected were a Microsoft Xbox 360 Wireless adapter, and Logitech K400r wireless USB keyboard.
Good luck out there..