URL-encoded square brackets in an internal link are not correctly parsed into a link. External links ARE correctly parsed.
These work, and are correctly parsed into external links:
These work, and are correctly parsed into internal links:
These do NOT work, and not parsed into internal links:
The only ones that do not work are internal links with URL-encoded square brackets. The culprits are the left bracket [ encoded as %5B and the right bracket encoded as %3A.
It does not seem to matter how many, in what order, etc. If %5B or %3A exist in the internal link URL, the link will not be parsed into an internal wiki link. The problem does not occur for external links.
I marked this bug as "major", but not "critical", because the bug can be worked around by changing internal links to external links (with the full URL) until the bug is fixed. However, since only a few of the most proactive site administrators are likely to read this bug report, this should be considered a critical bug for ordinary MediaWiki users, and casual administrators that don't read bug reports.