Same issue here. With an Ubuntu guest host I see this after attaching the yubikey:
[ 24.626777] usb 2-2: new full-speed USB device number 2 using xhci_hcd
[ 24.775061] usb 2-2: New USB device found, idVendor=203a, idProduct=fffe, bcdDevice= 1.01
[ 24.775066] usb 2-2: New USB device strings: Mfr=1, Product=2, SerialNumber=3
[ 24.775066] usb 2-2: Product: Virtual USB1.1 HUB
[ 24.775067] usb 2-2: Manufacturer: Parallels
[ 24.775068] usb 2-2: SerialNumber: PW3.0
[ 24.775274] hub 2-2:1.0: USB hub found
[ 24.775302] hub 2-2:1.0: 15 ports detected
[ 25.066773] usb 2-2.6: new full-speed USB device number 3 using xhci_hcd
[ 25.186750] usb 2-2.6: New USB device found, idVendor=1050, idProduct=0406, bcdDevice= 5.12
[ 25.186754] usb 2-2.6: New USB device strings: Mfr=1, Product=2, SerialNumber=0
[ 25.186755] usb 2-2.6: Product: YubiKey FIDO+CCID
[ 25.186756] usb 2-2.6: Manufacturer: Yubico
[ 25.198880] hid-generic 0003:1050:0406.0004: hiddev3,hidraw3: USB HID v1.10 Device [Yubico YubiKey FIDO+CCID] on usb-0000:00:03.0-2.6/input0
[ 25.218852] xhci_hcd 0000:00:03.0: ERROR Unknown event condition 12 for slot 4 ep 6 , HC probably busted
[ 25.318955] xhci_hcd 0000:00:03.0: ERROR Unknown event condition 12 for slot 4 ep 3 , HC probably busted
[ 30.324334] xhci_hcd 0000:00:03.0: ERROR Unknown event condition 12 for slot 4 ep 3 , HC probably busted
[ 35.329519] xhci_hcd 0000:00:03.0: ERROR Unknown event condition 12 for slot 4 ep 3 , HC probably busted