I noticed this behaviour in someone else's edit. It appears that they had habitually wikified a term despite the fact that they were including it as the text of an external link. I realise this shouldn't be supported, but the behaviour that it exhibits should probably be considered as not "doing the right thing".
What it does is hard to explain, so here's a diff to a WP:Sandbox edit demonstrating it:
This doesn't really break anything or pose any security issues (that I can think of), but the code handling wikitext rendering should probably not try to wikify double-square-bracket-delineated text in external links anyway.
Kynnin Scott http://en.wikipedia.org/w/index.php?title=Wikipedia%3ASandbox&diff=11983... oldid=11983377