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This is citrus brown rot. There isn't a lot you can do, as most treatment is preventative. In some cases wettable sulfur, or iron sulphate can help, or copper sulfate as well. This article will give you more information: https://www.gardeningknowhow.com/edible/fruits/citrus/citrus-fruit-brown-rot.htm

This sounds like a fruitworm. This article will help: https://www.gardeningknowhow.com/edible/fruits/fegen/how-to-control-fruitworms.htm

Any citrus is best pruned after the fall harvest or anytime during early flowering. This article will help: https://www.gardeningknowhow.com/edible/fruits/oranges/pruning-orange-trees.htm

Almost all citrus will have thorns at some point in their lives. Now this comes with a few more questions. Does the majority of your tree have little to no thorns? If this is the case, and there is a branch with more than usual, then this could be coming from beneath the graft point. If this is the case then you can prune the "suckers" out as needed. If this is from seed, then I would expect to see thorns all the way until they are old enough to start bearing fruit. If this is just a branch that is in the way of the rest of the tree then you can cut it out at almost any time. It is best to do so when the tree is not flowering.

Here is a collection of citrus articles to help you start identifying citrus and their issues: https://www.gardeningknowhow.com/edible/fruits/citrus/

The most likely thing that is happening, is that you have a few branches growing from beneath the graft point. This is pretty common. You can actually cut the branches that are producing these odd fruits. If you don't mind them being there, then you can just leave them as a little extra gift from the plant.

Unfortunately, if you do not know the specific orange, you may never see a flower or fruit. Many store bought oranges are pollinated with wild oranges, and will depend on the farm. Container grown oranges from seed can take 6 years or more to bear the first flower. Then another few to be able to produce a fruit. There are just too many factors to be able to tell right now. If you are growing one from seed, unless you know that it is a true to type variety, such as the blood orange, then you should not expect a fruit from the tree in its lifetime.

Here is an article for growing oranges in container: https://www.gardeningknowhow.com/edible/fruits/oranges/orange-tree-container-care.htm