I just got confused by your “user error” suggestion, because I don’t see how this qualifies as one.
Because you're both claiming to understand the failing of reddit's UI and claiming the same UI as a reliable indicator of all comments getting deleted. Rather, it seems some comments were likely missed because of the shitty UI. Relying on reddit's UI for this is the specific user error to which I was referring. I hope that's clearer.
First, the Reddit API is broken, because the select query sent by the deletion tool receives less than a full set (as if there was an implied LIMIT clause on the server side). This leads the deletion tool to erroneously announce it has processed all comments.
I don't see anywhere that goes into what redact.dev does behind the scenes (closed source on something like this is a huge red flag to me, but more relevant here is that there's no indication whether it was using an app-specific api key or just using a hidden browser under the hood), though I do see where the reddit service page states:
Reddit stores posts in comments in a weird way. If you’re trying to delete thousands at once, we may not be able to find all of them.
You also mentioned that's how you confirmed all your comments were deleted. One could argue using a tool that admits it can't see all your comments to confirm whether your comments are all deleted could be considered an error as well.
There is literally no mechanism to find leftover comments...
Best approach I've seen that's still standing for a post-API reddit is using the GDPR request as input for one of the tools using it, so it's not relying on the janky UI.
Kinda comes with being on /m/redditmigration, no?