Nectar is earned from your flowers and is used for sending your Explorers on Expeditions! Tap on the Nectar Collector on the outside of the hive to collect - it will display how many nectar are waiting to collect, as well as the maximum you can collect. This means if the timer is showing nectar collection make sure you check in to collect your nectar so the tube can refill. The Nectar Collector will tell you when no flowers are ready or will say how long until the tube is full when your flowers are actively being harvested. As you progress, you can increase the Nectar Collectors maximum capacity through Expeditions and the research station.
Do not worry as you are never losing out on Nectar, if your Nectar Collector is full the bees will just take a break from collecting until there is room in the Nectar Collector again!