Hmm, on my motherboard I had to disable spontaneous wake by adding to /etc/udev/rules.d/:

  ACTION=="add", KERNELS=="0000:00:01.1", ATTR{power/wakeup}="disabled"

And my Logitech Bolt receiver wakes multiple of my Linux computers instantly, I don't know why it doesn't do that on Windows and haven't tried doing a USB capture (and don't know what equipment I'd need to try it out, logic analyzer? Glasgow?). In the meantime I've added a rule to block that:

  ACTION=="add", SUBSYSTEM=="usb", DRIVERS=="usb", ATTRS{idVendor}=="046d", ATTRS{idProduct}=="c548", ATTR{power/wakeup}="disabled"