I just tried it for myself, it only made 63 requests to delete 12 comments. These were in my profile, they're ones that have reappeared after being deleted previously.
Meanwhile, if I look in my GDPR files up to where I've got so far with shreddit, the comments are still there, completely untouched.
Maybe you don't have too many comments, so you're within the 1,000 comment limit across your different lists? It's impossible to be sure without having the direct links, either from a GDPR request or the Pushshift backup.