That does rule out the creators, yeah.

When you say it happens instantly, do you mean that you instantly get a "Post deleted" notification of some sort, or just that you hit "Reply" and the post never shows up?

I ask because there's a blog I comment on sometimes that occasionally pretends like it's posting my comment, but then the comment doesn't appear. My first assumption was that I was encountering some kind of moderation filter, but it turns out I wasn't. That blog just has poorly designed error handling. If I take too long to write my comment, the session expires. That's fine and normal, but the problem is that the blog software doesn't bother to warn me before posting, and it doesn't explain itself after the post fails, so it creates confusion. Once I realized what was going on though, I realized I could just hit "Back" to recover and copy the comment I wrote, reload the page to get a fresh session, paste the comment, and hit "Reply." Works totally fine that way.

Maybe YouTube is doing something similar and dropping attempted comments due to expired tokens or shoddy networking? It would explain why it seems so random and nonsensical.

If it really is bad auto-mod systems, there probably isn't much you can do about it besides complain to YouTube. Any workaround that would be easy for you to use would be equally easy for the spammers and trolls to use, and is therefor not likely to remain a usable workaround for long.