When using Markdown format if the message content a markdown link to an existing issue, the result is that we have a link to the issue with a text like `[issuexyz](issuexyz)`.
This is because call to `hyper_re.sub` call the method for every non-overlapping occurrence of the pattern.
I think a possible option is to use rewrite the regexp to not overlap (as suggested by https://stackoverflow.com/questions/5616822/python-regex-find-all-overlapping-matches#comment81721360_5616822).
I think also that the problem exist for other format using the same regexp.