In the e-mail notifications for a new comment added to a task, any URLs in the text of the comment get Welcome added around them, even if said square brackets weren't in the original comment.
This is needless, and means that some e-mail clients don't auto-link the URL.
I can't reproduce this. Can you make a comment on this task which you believe reproduces the issue?
[[ ]] is part of Remarkup, so it has to be typed in directly by the comment author (making the URL appear normal in the comment if they didn't name the link). We don't convert these strings.