Almost every fig tree that I have seen has these hollow holes in branches, etc. Fig branches are really tubes filled with pith. The pith rots away and leaves behind a hollow section of the branches. As your tree grows and puts out new wood, I would prune/trim away all those old dead sections back to the nearest live wood. This new fig tree of yours will look completely different within a few years, and you will be surprised at how much new wood will be growing from the original branch structure, and main stem. Let the tree grow out after eliminating any wood that is obviously dead. Try not to be concerned. You will learn how and where to prune your tree branches to avoid this kind of thing.
Look at your first photo showing the whole tree. See that large, low-growing main branch? If it were me, I'd air-layer that section, and eliminate the possibility of that second leader, splitting away from the main trunk in the future. If you air-layer that low, side branch, you will then have two trees. Growing on its own roots, that side branch will probably give you figs next season.
Hope you replant this tree into a larger container, or plant it in the ground. Now, is the time to do this.
Nice tree. You'll have figs to eat this summer. Good luck, and happy growing.
Frank