Most bikes determine their charge by voltage of the battery pack. Granted there are other things in their sometimes twisted formulae to do so but the voltage is a BIG determination. With that, it's not uncommon for a bike to drop a percent or two sitting like that.
A. The batteries settle in, so the surface charge of a fresh charge goes away as they balance and settle out
B. The temperature of the cells drops, since no more current flow = no more heat generated, this causes temperature and voltage to drop slightly, along with perceived charge.
C. The bike got some stuff going on, it IS using electricity, so is sucking a bit off the top of the battery. The power dissipation of a battery is not quite linear and at the very top, (and very bottom) there isn't a hell of a lot of power density, so yah, that clock, or checking for internet etc etc every 30 seconds ever a day or can make it drop 0.1 volts ish or whatever, and make it think the battery is slightly discharged from what it last called 100 percent.
D. It got cold outside, and temperatures are more towards the lower end of the batteries useable range, this can cost you a few percent.
Then again, you could also have an older battery, with a cell getting weaker and it's pulling it down or self discharging a lot faster than when brand new.
Most bikes have some sort of 'storage' mode you can slap a charger on them and it'll keep them charged up where they need to be over the weekend, work week, winter months, etc etc.
Aaron