Like many websites, we have more than one domain name: widget-shop.com, widget-shop.co.uk, widgetshop.eu etc. etc. And, like any decent site we ensure that they correctly redirect to our principal domain with a 301 code - so www.wiget-shop.co/foo.html => www.widgetshop.co.uk/foo.html.
For a short period five months ago, we made the mistake of not ensuring one of our domains properly redirected to our common domain. So our entire site was duplicated: www.widget-shop.com gave exactly the same results as www.widgetshop.co.uk
Pretty stupid oversight. Google indexed widget-shop.com in all its glory. The mistake was spotted after six days, and the correct 301 redirects put into place. Through Webmaster tools we let Google know that widget-shop.com was an alias for our principal domain. Double-checked it was set up right using 'fetch as googlebot'. And crossed our fingers.
The first thing was saw was that our main site (widgetshop.co.uk) now had as its principal linking domain widget-shop.com. Every link in Google's cache for the wrong domain was now (correctly) redirecting to our principal domain. Result: I have over 6000 links from widget-shop.com to widgetshop.co.uk. And not only are they not going away... five months on they're still growing.
The result was a collapse in our rankings. Traffic down 50% and all sorts of search engine pain.
I think what is happening is that from time to time Google still looks at what it cached for widget-shop.com, finds new links it hasn't bothered with before, finds they're redirecting to widgetshop.co.uk and add them to the list of linking domains. It's certainly not prepared to believe that they're the same thing.
I can still see all those pages from widget-shop.com in the Google cache if I do a site search - and the canonical meta tag correctly shows widgetshop.co.uk/foo.html. At least we got that right, but it's made absolutely no difference. In fact nothing has. There's nothing more I can do about this utterly bogus domain, but it pains me to watch, every week, its links growing and growing. I can't be absolutely sure it's the cause of a rankings drop, but the slow strangulation of our organic results since this occurred makes me think it's probably connected.
So, be careful with those domain name aliases, and don't end up like us!