What causes battery calibration errors?

[BlackZeppelin]

Occasionally I notice errors in battery calibration. For eg, tonight I charged my S5, turned off wifi and bluetooth plus greenified all my downloaded apps and one system app, YouTube. An hour later the phone registered as 98 percent. I thought that was really odd so I plugged it back on my charger and in about 10 secs it registered fully charged. So obviously it was not 98 percent, but still 100 percent.

What causes these types of battery calibration errors and how have you found the best way to recalibrate? I am not really a fan of any 3rd party app that requires you to fully charge then fully discharge as that is not good for Li ion batteries.

Thanks.