Being the only person on my instance subscribed to certain communities on other instances, I am pretty sure it is a federation issue. When I look at the comment counts for the same post on two different instance accounts, they are not the same. They often share the same comments, but not all of them. Sometimes the number shown below the post reflects only the comments from the instance you’re viewing it on, sometimes it shows all of them.
For example, looking at the Baldur’s Gate 3 community on Lemmy World when logged on to Lemmy World, the top post has about 36 comments but counting them in the post there are only 30. 3 of those comments are mine, and they aren’t being shown to my Lemmy World account. When I view it from Yiffit, only my 3 comments appear, while it also says there are 36 total. According to the subscriber count, I am the first person on Yiffit to subscribe there, and that was about an hour ago.
Different comment counts between instances is a federation thing, yes. But showing a number of comments different to the comments shown on the same instance, not.
There are reasons for missing comments, especially on communities from lemmy.world right now. But that’s not what is being reported. A federation message for a post does not contain the number of comments (and that would be a totally pointless property to send). It’s also quite common that certain comments don’t make it over federation.
The screenshot is showing a comment count without comments, that means the instance has one comment locally but for some reason is now showing it. That’s not a federation thing.
