Its a problem, and at the same time a feature. For example, you can have two communities named !news, that pertain to completely different topics based on their instance:
This also isn't unique to lemmy, since reddit too had tons of duplicate communities for the same topics.
Just like on reddit, the network effect will run its course here: unavoidably there will be a lot of cross-posting on duplicated communities, until people center around their favorites, based on quality of content.
There are a few tools out there too, like https://lemmyverse.net/communities , that can help people find communities to subscribe to.
Overall tho, I'm against the concept of "combining / merging communities" that are run on different sites by different people. These should be curated and controlled by the people who created them.