Consider this URL:
It has one parameter, foo, with the value "bar&baz=quux+quux". Place this in an article and the externallinks table will contain this URL instead:
This has *two* parameters, foo with the value "bar" and baz with the value "quux quux".
Then try this URL:
The value of foo is "%xx". But put it into an article, and externallinks will contain this URL instead:
That's not even valid.
The problem lies in Parser::replaceUnusualEscapesCallback, it will unescape %25, %26, %2B, and %3D despite these all having special meaning in a URL when unescaped. I see a similar-sounding problem was reported in bug 4781, which was closed as "fixed" with no reference to the revision in which it was fixed. Bug 40267 also touched upon this issue, but these real problems appear to have been overlooked since the reporter there focused on the unescaping of various safe characters rather than only these unsafe ones.