Great Building bonuses are usually available several times per day. As you use the bonus up, it will eventually disappear.
So if you've used all charges, the bonus will not show up in your city on that day again. You can see the number of remaining charges in your town hall, on the Boost overview screen. If you can not use the bonus on that day any more, the bonus icon will not appear.
You can see this in action with the remaining bonus for the Lighthouse of Alexandria showing in the video below: