I was having a hell of a time resolving this issue myself and was almost ready to abandon using Retroarch as my Dolphin replacement, until I discovered I had the wrong drivers selected for my system. My solution:
1. Start Retroarch.
2. Hit <F5> to open Desktop Menu.
3. Click <View>-<Settings>.
4. At the top/Left is a Drivers catagory. My settings are as follows:
Input: dinput
Joypad: xinput
Video: vulkan
Audio: xaudio
Audio Resampler: sinc
Camera: null
Location: null
Menu: xmb
Record: ffmpeg
MIDI: winmm
These are the only settings which the core would accept without crashing Retroarch.
It works with Gamecube and Wii games on my end.