Those extra long branches/shoots are likely water sprouts; they are a result of your being a little too kind to your tree. Usually they will have larger leaves and large thorns. It is best to prune them back to the general level of the canopy; and then they will revert to normal growth. Leaving them makes little sense unless you are just trying to increase the overall size of the tree. Water sprouts do not produce fruit.

I usually don't prune my really young trees for the first 2 years after purchasing. I want to see what it does first. After that, once it gets to the width I want, I have to prune or pinch or it won't fit through my door frame for winter storage.

If you don't prune or pinch back, those long limbs may produce fruit and be too heavy and fall down. I bit the bullet and pruned some of my trees lightly because in the long run, I am setting up the foundation for heavier fruit production.

Thanks very much John and Denise. Your explanations help a lot.

Water sprouts will not produce fruit while they are aggressively growing but even if left alone they will branch at some point and they will revert to 'normal' canes. Despite this, it is better if one either removes them completely, if the tree is already mature, or as suggested above, if the tree is small and young and sparse of canes prune them to an eye and they will branch out from there.

In general, one should not overdo pruning citrus, even potted ones. Trying constantly to achieve a vase shape of canopy like in a stone fruit tree, will result in branches only fruiting at the top because branches leaning at less than 45 degrees will exhibit apical dominance of the tip eyes only. Letting the tree acquire some reasonably long sideways branches will result in lateral growth stemming out of them and fruiting all along the branches. If one has grown climbing roses one will know what I'm talking about.

Flowers on citrus are formed from new growth. Strong up growth should be cut short to induced side branches. Some citrus like mandarins need to grow bushy, they have a tendency to overbearing. On long branches they might reach the ground, a no no. What the hell do I know about citrus, I am into persimmon. As a citrus amatuer like a few others I am doing more than satisfying.