For example, I’m on Lemmy.sdf.org and I joined the Apple@lemmy.ml community. But there are many missing articles and comments. If I browse directly on Lemmy.ml for the same article there ~90% of comments are missing.
https://lemmy.ml/post/1152794 has 26 comments https://lemmy.sdf.org/post/11232 has 0 comments
They do. However, it’s only after federation has been established between two communities.
After a while, these newer communities will be federated in and everyone will be connected.
As lemmy.ml is the oldest community, it also has the most history (as the newer instances don’t currently get the history).
This will likely be fixed at some point.