Found an interesting unusual workaround for the problem: if I move my mouse during resume all USB ports seem to work normally. I have a wireless Logitec mouse with USB receiver:
/: Bus 04.Port 1: Dev 1, Class=root_hub, Driver=xhci_hcd/2p, 10000M
/: Bus 03.Port 1: Dev 1, Class=root_hub, Driver=xhci_hcd/4p, 480M
|__ Port 2: Dev 4, If 0, Class=Human Interface Device, Driver=usbhid, 12M
|__ Port 2: Dev 4, If 1, Class=Human Interface Device, Driver=usbhid, 12M
/: Bus 02.Port 1: Dev 1, Class=root_hub, Driver=xhci_hcd/2p, 10000M
/: Bus 01.Port 1: Dev 1, Class=root_hub, Driver=xhci_hcd/4p, 480M
|__ Port 3: Dev 6, If 0, Class=Video, Driver=uvcvideo, 480M
|__ Port 3: Dev 6, If 1, Class=Video, Driver=uvcvideo, 480M
|__ Port 4: Dev 7, If 1, Class=Wireless, Driver=btusb, 12M
|__ Port 4: Dev 7, If 0, Class=Wireless, Driver=btusb, 12M
in dmesg during ‘bad’ resume:
...snip...
34260.540547] PM: resume devices took 2.421 seconds
[34260.540644] OOM killer enabled.
[34260.540645] Restarting tasks ...
[34260.540730] usb 1-3: USB disconnect, device number 2
[34260.540730] usb 3-2: USB disconnect, device number 2
[34260.546354] done.
[34260.555763] PM: suspend exit
[34260.608705] usb 1-4: USB disconnect, device number 3
‘good’ resume:
[37981.614829] PM: resume devices took 0.340 seconds
[37981.614889] OOM killer enabled.
[37981.614890] Restarting tasks ... done.
[37981.634136] PM: suspend exit
[37981.731684] usb 1-3: new high-speed USB device number 4 using xhci_hcd
[37981.731684] usb 3-2: new full-speed USB device number 3 using xhci_hcd
[37981.883620] usb 3-2: New USB device found, idVendor=046d, idProduct=c52f, bcdDevice=30.00
[37981.883625] usb 3-2: New USB device strings: Mfr=1, Product=2, SerialNumber=0
[37981.883626] usb 3-2: Product: USB Receiver
[37981.883627] usb 3-2: Manufacturer: Logitech
[37981.898783] logitech-djreceiver 0003:046D:C52F.0005: hidraw0: USB HID v1.11 Mouse [Logitech USB Receiver] on usb-0000:06:00.4-2/input0
[37981.954341] logitech-djreceiver 0003:046D:C52F.0006: hiddev96,hidraw1: USB HID v1.11 Device [Logitech USB Receiver] on usb-0000:06:00.4-2/input1
[37981.975612] usb 1-3: New USB device found, idVendor=04f2, idProduct=b6bb, bcdDevice= 0.05
[37981.975617] usb 1-3: New USB device strings: Mfr=3, Product=1, SerialNumber=2
[37981.975619] usb 1-3: Product: HP Wide Vision HD Camera
[37981.975620] usb 1-3: Manufacturer: Chicony Electronics Co.,Ltd.
[37981.975621] usb 1-3: SerialNumber: 0001
[37982.010940] usb 1-3: Found UVC 1.00 device HP Wide Vision HD Camera (04f2:b6bb)
[37982.012553] logitech-djreceiver 0003:046D:C52F.0006: device of type eQUAD step 4 DJ (0x04) connected on slot 1
[37982.103938] logitech-hidpp-device 0003:046D:4057.0007: HID++ 4.5 device connected.
[37982.119877] input: HP Wide Vision HD Camera: HP Wi as /devices/pci0000:00/0000:00:08.1/0000:06:00.3/usb1/1-3/1-3:1.0/input/input32
[37982.179327] Generic FE-GE Realtek PHY r8169-0-200:00: attached PHY driver (mii_bus:phy_addr=r8169-0-200:00, irq=MAC)
[37982.233891] usb 1-4: new full-speed USB device number 5 using xhci_hcd
[37982.393755] usb 1-4: New USB device found, idVendor=8087, idProduct=0029, bcdDevice= 0.01
[37982.393762] usb 1-4: New USB device strings: Mfr=0, Product=0, SerialNumber=0
Hope that helps.