If so, is there any way to bring communities with the same purpose (or even same name) on different instances together? If not, how can we prevent fragmentation of these communities?
I see this as a feature and not a bug. A reddit sub can be taken over by a small but vocal group of users or mods rendering the sub distasteful to the general public. Very little can be done once that happens but here you can "vote" with your subscription.
One will become more popular over time.
Even still, one might attract one kind of community and the other a different kind of community. That's sort of why there are different instances right? It's due to a fundamental difference between Lemmy and Reddit.
Yeah, I think this is going to be an issue/ something that the community is going to have to think about. It actually makes more sense for lemmy instances (like wallstreets.bet) to focus on particular subcultures/ types of communities, rather than being catch alls. This has a couple advantages in that you can replicate some of the structure of reddit (like having tagged posts), and it allows federation to focus on connecting to things that makes sense. This way resolves the duplicity issues.