Earlier quoted context omitted.
I used Power Delete Suite to remove all comments from all public and private subs. They all came back today. So I re-deleted them again. I suspect it's more likely the site didn't process the deletions properly, rather than maliciously bringing them back, or as you suggest, that they were private. Edit: It's possible that the deletion only worked on public posts, after all, it seems?
I've got a decade old account on which I've made a habit of manually deleting comments older than 6 - 9 months, since they get so little visibility and there's no value in leaving a breadcrumb trail. Checking just now I see that comments up to 3 - 4 years old have been restored. I'm not going to speculate as to why (beyond agreeing it's more likely to be incompetence than malice) but in my case at least there are def…
For most users this isn't going to be a problem but my guess is there is a rather big chance for a number of the comments that were restored there were really good reason why they were deleted and now Reddit are responsible for them being online again.