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
This is my understanding as well, after using a number of different instances over the last few months.
I believe this issue will mostly sort itself out in the future as the federated network becomes more “connected”
A new instance connecting to an existing one will have content from the established instance missing, but as time goes on that content becomes a smaller portion of the overall content.
I anticipate some development on this issue in the near future anyway, perhaps cached content that is able to be “pushed” to a requesting instance.