This post earlier in the day I think had some good information on this subject.

There is a lot of syncing going on across instances so part of it could be due to some comments just not being federated yet or it could be that the one with less is not federating with as many other instances and missing some users that federate to the other.

Comments are pushed out by the community's server, they're not pulled in by yours. So if you're missing comments from communities hosted on lemmy.ml for example, it may be that lemmy.ml is overloaded and not sending out comments to the fediverse properly.

The other common issue with missing comments and posts is misconfigured language settings in your profile. You need to make sure at least Undefined and English are both selected, lots of people only have English selected which will make a lot of posts hidden.

The other 4 commenters here got it right. I’ll add that would think this could be improved in the future.