There is a possibility of some other USB item, or anything that may share a powered USB hub (?)
or the wi-fi router in the vicinity, could awaken the sleeping computer. In cold weather, if I walk into
the same room where the computers are sleeping and take off a static-charged synthetic fabric
jacket, that alone can wake up at least one or two; out of three.
Awakening at night, could be attributed to a change in electrical power from the utility grid.
Mine use a UPS backup power supply that automatically switches, on change in line voltage.
The built-in software in OS X will awaken the computer in preparation of automatic shutdown.
Other items in the vicinity could affect the sleep cycle, and could appear in the Console log as
a USB inspired wake-event. Even the trackpad in a portable computer is a USB device. Some
wireless items also share the same bus in the computer. Troubleshooting can begin if you go
about isolating these other peripheral items. A microwave oven nearby or a cordless house
phone may send out a wake-up due to these frequencies having an effect on the Mac.
In other macs where a trackpad or other device is being used, the ignore input option helps.
Since I usually have at least two Macs, sitting around asleep when not in use, for up to
six months at a time, the issue hasn't been a great one. Unless I move or accidentally hit
a sleepy mouse; then it squeeks a wakeup to the Mac...
Good luck in this matter! 🙂