The short answer is that your phone will never get charged fully with the stock kernel. Some phones now try to protect the life of the battery because Li-ion have a limited charge/recharge cycle count. Theoretically, by never 'fully' charging the battery and keeping it between 90-100%, it should make it last longer. You can install what's known as an SBC kernel to force the charge cycle to 100%, but depending on your beliefs on what can happen when you overcharge lithium-ion batteries, it may not be without risk of shortening the life of your battery or having it go up in flames (depending what you read, lol). Do some research and see if that last 5% or so is worth it for you.
For the long answer, google 'SBC kernel' and read about it, or take a look at this link:
Are SBC kernels worth it? | TalkAndroid.com