Estimates != 100% project time spent.

I'd say the main issue is misunderstanding of concept we are planning between business and tech people. Those groups think so differentely. We use Planning Poker tool - https://scrumhub.it/ for each user story, but still there area projects unestimated with strongly extended timeline compared to initial estimates. But on the other hands mostly it happens when business add new features, change requirements and the wheel comes full circle, we do retro and it is what it is :)