It's a difficult one. There are ongoing federation issues just about everywhere even within Lemmy and Kbin themselves, so once we get to talking cross-compatibility the problem appears to be even worse.
It has got drastically better since I first joined, so there are clearly investigations underway, but there's still a fair way to go until it's totally reliable.
That said, just to clarify, when you say you're "unable to reply to them" do you mean because their comment doesn't show up on your side, or because you get some kind of error or other weird behaviour when you try to reply?