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As a safety feature, the phone runs from the battery while on the charger. The phone battery will never trickle charge.
So, what happens is this - when the phone reaches full charge, the green light (most phones) come on and the battery shows 100% - and it stops charging. Then, servicing whatever functions are being used in background (or foreground if you're using your phone while on the charger), the battery is used and starts to discharge until it's at the manufacturer's set point, anywhere from 92 to 96%, and then begins charging again.
If you graphed it over time, it would look like a long roller coaster of battery power going at the low from the 90s to the top at 100% - it would look pretty much like a sine wave.
When you pull your phone from the charger, it will say 100% but it will really be anywhere along that curve from the 90s to 100%. Only after running normally for maybe 15 minutes (or rebooting) will the true battery percentage show.
This is identical to how laptops charge and operate - it's the same safety technology.
In the laptop world, this leads to snake-oil sales to replace perfectly good batteries, in the phone world, this leads to no end of phoney battery tweaks. You'll think you're using up to 8% of your battery in 15 or 20 minutes or that something is broken in the read-out - when it's just the design.
If you pull your phone off the charger the instant it turns green, you'll find it consistently showing 99~100% charge.
The actual percentages are calculated by process taking a sensor reading of the battery's mV state and comparing that to a battery calibration file, and then calculating percentage. That same calibration file is slowly updated over time as the system continuously learns about the actual battery installed.
For that reason, new phones seem to get longer life within the first few weeks to a month of use. It's simply the calibration file getting - well - calibrated.
The benign battery tweaks simply force that calibration to occur more quickly, but really isn't a problem if you skip that.
If you root your phone and replace the software, you can get a really screwed up battery calibration file, so rooter use a calibration tool to erase the file so it can be rebuilt properly over a short time's worth of use.
Otherwise, avoid things like tips telling you to drain the battery completely several times before use. Usually that sort of forced use can be accompanied by a rapid heat build-up and heat is not a battery's friend.
That's the whole story - hope this helps!
