Are you having any issues with devices not working or is it just simply a device manager issue? If you are NOT being limited by functionality, my best recommendation if "@CompulsiveBuilder"'s advice didn't answer it is, just disable the devices. If you are NOT impeded by the lack of them, they are likely just tag along devices Windows found in something else. The PCI controller is almost always a nuisance on installs using higher end boards. I've got an Asus and Gigabyte board BOTH looking for said driver. Been using the machines for anything and everything and just disabled the device. No problems at all. Bus controller is seen on one of my boards (Gigabyte) but also disabled with no negative results.
Nope, doesn't sound like you've missed anything at all, weird stuff like that happens. Just have to learn from it and go on. If it's an issue, disable them, if it isn't, do as you wish but, there really isn't anything (driver) you could find to take care of the issue. Just happens.