OK, it isn't really a problem and is working correctly. You have comment "threading" active, which means that people can make a general comment on the entire thread (top level comment), or they can reply directly to other comments that have already been made.
Example: Go to comment 59 and it is dated May 1. The comment right below it is a reply to that particular comment and it is dated May 22. If you will notice, the reply comment is slightly indented and also has no number associated with it.
The same with #63
Original comment May 2
First reply to it on May 2 - indented
Second reply to it on May 3 - indented
With the theme you are using, the numbered comments are original top-level comments on the post and those are in order by date. Replies to those top level comments are indented below them.