Basically, what you're describing is a feature, not necessarily a bug to be resolved. Some apps may decide to implement ways to compile them all, but by design, instances can/should have duplicate-named communities.

Imagine two instances with very different idealogies that both have a c/general community. One is discussing their next hate crime, while the other is discussing the bake sale at the local HS basketball game. Merging those would be a mistake, right?

I do see where you're coming from with this question though. I did wonder which communities to follow when I first joined, but now I follow a few same-named ones and appreciate the differences between them.